rs1862788

Variant names:

• chr16-87302820-G-A
• rs1862788
• NM_001195124.3:c.*237C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-87302820-G-A
• chr16-87302820-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001195124.3(C16orf95):​c.*237C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 547,198 control chromosomes in the GnomAD database, including 1,680 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.076 (1316 hom., cov: 32)
  • Exomes 𝑓: 0.014 (364 hom.)
• Consequence: C16orf95 NM_001195124.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 publications found

Genes affected

C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

ENSG00000131152 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001195124.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	NM_001195124.3	MANE Select	c.*237C>T		3_prime_UTR	Exon 7 of 7	NP_001182053.1	H3BNZ7
	C16orf95	NM_001195125.3		c.*296C>T		3_prime_UTR	Exon 5 of 5	NP_001182054.1	Q9H693
	C16orf95	NM_001256917.2		c.*296C>T		3_prime_UTR	Exon 5 of 5	NP_001243846.1	A0A087X224

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	ENST00000567970.2	TSL:5 MANE Select	c.*237C>T		3_prime_UTR	Exon 7 of 7	ENSP00000455079.2	H3BNZ7
	C16orf95	ENST00000253461.8	TSL:1	c.*296C>T		3_prime_UTR	Exon 5 of 5	ENSP00000253461.4	Q9H693
	C16orf95	ENST00000931586.1		c.*237C>T		3_prime_UTR	Exon 6 of 6	ENSP00000601645.1

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11475 AN: 152082 Hom.: 1305 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00538

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00495

Gnomad OTH AF: 0.0647

GnomAD4 exome AF: 0.0142 AC: 5594 AN: 394998 Hom.: 364 Cov.: 3 AF XY: 0.0129 AC XY: 2695 AN XY: 209084

African (AFR) AF: 0.242 AC: 2658 AN: 10982

American (AMR) AF: 0.0219 AC: 404 AN: 18416

Ashkenazi Jewish (ASJ) AF: 0.0350 AC: 418 AN: 11938

East Asian (EAS) AF: 0.0000379 AC: 1 AN: 26360

South Asian (SAS) AF: 0.00683 AC: 300 AN: 43904

European-Finnish (FIN) AF: 0.00166 AC: 41 AN: 24696

Middle Eastern (MID) AF: 0.0372 AC: 62 AN: 1668

European-Non Finnish (NFE) AF: 0.00482 AC: 1131 AN: 234622

Other (OTH) AF: 0.0258 AC: 579 AN: 22412

GnomAD4 genome AF: 0.0758 AC: 11531 AN: 152200 Hom.: 1316 Cov.: 32 AF XY: 0.0725 AC XY: 5396 AN XY: 74438

African (AFR) AF: 0.250 AC: 10359 AN: 41478

American (AMR) AF: 0.0339 AC: 519 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00580 AC: 28 AN: 4826

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10616

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00495 AC: 337 AN: 68024

Other (OTH) AF: 0.0640 AC: 135 AN: 2110

Alfa AF: 0.0265 Hom.: 532

Bravo AF: 0.0851

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.6
DANN	Benign	0.80
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1862788; hg19: chr16-87336426;