chr16-64223641-G-A

Variant names:

• chr16-64223641-G-A
• rs318218
• ENST00000769474.1:n.123+28177C>T

Variant summary

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

The ENST00000769474.1(ENSG00000261028):​n.123+28177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,152 control chromosomes in the GnomAD database, including 515 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 0.077 (515 hom., cov: 32)
• Consequence: ENSG00000261028 ENST00000769474.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

Genes affected

ENSG00000261028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261028	ENST00000769474.1	n.123+28177C>T		intron_variant	Intron 1 of 1
ENSG00000261028	ENST00000769475.1	n.97+2136C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0768 AC: 11674 AN: 152034 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.0616

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0767 AC: 11677 AN: 152152 Hom.: 515 Cov.: 32 AF XY: 0.0736 AC XY: 5478 AN XY: 74396

African (AFR) AF: 0.0530 AC: 2202 AN: 41510

American (AMR) AF: 0.0594 AC: 907 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 340 AN: 3472

East Asian (EAS) AF: 0.0672 AC: 346 AN: 5148

South Asian (SAS) AF: 0.0615 AC: 296 AN: 4816

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10624

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6853 AN: 67982

Other (OTH) AF: 0.0695 AC: 147 AN: 2114

Alfa AF: 0.0227 Hom.: 16

Bravo AF: 0.0762

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.087
DANN	Benign	0.25
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs318218; hg19: chr16-64257545;