rs16850360

Variant names:

• chr4-74006728-A-G
• rs16850360
• ENST00000669992.2:n.1035-167A>G

Variant summary

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

The ENST00000669992.2(ENSG00000287037):​n.1035-167A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,294 control chromosomes in the GnomAD database, including 232 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 0.044 (232 hom., cov: 32)
• Consequence: ENSG00000287037 ENST00000669992.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 13 publications found

Genes affected

ENSG00000287037 (HGNC:58815):

LOC124900715 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669992.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287037	ENST00000669992.2		n.1035-167A>G		intron	N/A
	ENSG00000287037	ENST00000716529.1		n.311+7366A>G		intron	N/A
	ENSG00000287037	ENST00000769988.1		n.278+7366A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6656 AN: 152176 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0965

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.0300

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0437 AC: 6649 AN: 152294 Hom.: 232 Cov.: 32 AF XY: 0.0447 AC XY: 3331 AN XY: 74462

African (AFR) AF: 0.0102 AC: 425 AN: 41570

American (AMR) AF: 0.0964 AC: 1474 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.123 AC: 638 AN: 5186

South Asian (SAS) AF: 0.0623 AC: 301 AN: 4828

European-Finnish (FIN) AF: 0.0300 AC: 318 AN: 10606

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3027 AN: 68020

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0480 Hom.: 390

Bravo AF: 0.0507

Asia WGS AF: 0.0930 AC: 322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs16850360; hg19: chr4-74872445;