rs974474

Variant names:

• chr16-26792254-G-A
• rs974474

Variant summary

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

The variant allele was found at a frequency of 0.339 in 152,046 control chromosomes in the GnomAD database, including 9,462 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 0.34 (9462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 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

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51437 AN: 151928 Hom.: 9448 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.339 AC: 51479 AN: 152046 Hom.: 9462 Cov.: 32 AF XY: 0.347 AC XY: 25745 AN XY: 74294

African (AFR) AF: 0.222 AC: 9224 AN: 41502

American (AMR) AF: 0.454 AC: 6935 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.599 AC: 3087 AN: 5156

South Asian (SAS) AF: 0.514 AC: 2480 AN: 4822

European-Finnish (FIN) AF: 0.403 AC: 4249 AN: 10542

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23172 AN: 67950

Other (OTH) AF: 0.363 AC: 766 AN: 2112

Alfa AF: 0.346 Hom.: 37079

Bravo AF: 0.337

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.56
DANN	Benign	0.38
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs974474; hg19: chr16-26803575;