rs669684

Variant names:

• chr5-41574241-G-A
• rs669684

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 0.635 in 151,940 control chromosomes in the GnomAD database, including 31,627 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 0.63 (31627 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 1 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.786 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: 0.634 AC: 96310 AN: 151822 Hom.: 31583 Cov.: 31

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.635 AC: 96409 AN: 151940 Hom.: 31627 Cov.: 31 AF XY: 0.639 AC XY: 47450 AN XY: 74258

African (AFR) AF: 0.793 AC: 32895 AN: 41462

American (AMR) AF: 0.621 AC: 9473 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3771 AN: 5134

South Asian (SAS) AF: 0.758 AC: 3655 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5622 AN: 10558

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36508 AN: 67924

Other (OTH) AF: 0.647 AC: 1365 AN: 2110

Alfa AF: 0.574 Hom.: 101542

Bravo AF: 0.644

Asia WGS AF: 0.789 AC: 2742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.22
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs669684; hg19: chr5-41574343;