rs16968478

Variant names:

• chr15-74370470-A-G
• rs16968478
• ENST00000568496.3:n.4276A>G

Variant summary

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

The ENST00000568496.3(ENSG00000261821):​n.4276A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,128 control chromosomes in the GnomAD database, including 9,638 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 0.32 (9635 hom., cov: 32)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: ENSG00000261821 ENST00000568496.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 12 publications found

Genes affected

ENSG00000261821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568496.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261821	ENST00000568496.3	TSL:2	n.4276A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000302041	ENST00000783573.1		n.116-392T>C		intron	N/A
	ENSG00000302041	ENST00000783574.1		n.187-392T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48036 AN: 151988 Hom.: 9596 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.364 AC: 8 AN: 22 Hom.: 3 Cov.: 0 AF XY: 0.429 AC XY: 6 AN XY: 14

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 2 AN: 8

Other (OTH) AF: 0.750 AC: 6 AN: 8

GnomAD4 genome AF: 0.316 AC: 48139 AN: 152106 Hom.: 9635 Cov.: 32 AF XY: 0.319 AC XY: 23694 AN XY: 74366

African (AFR) AF: 0.560 AC: 23200 AN: 41456

American (AMR) AF: 0.254 AC: 3880 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2380 AN: 5180

South Asian (SAS) AF: 0.436 AC: 2102 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2101 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12571 AN: 67982

Other (OTH) AF: 0.297 AC: 627 AN: 2114

Alfa AF: 0.226 Hom.: 7722

Bravo AF: 0.331

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.87
DANN	Benign	0.38
PhyloP100		-0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16968478;

hg19: chr15-74662811;