rs3845624

Variant names:

• chr1-159248476-A-C
• rs3845624

Your query was ambiguous. Multiple possible variants found:

• chr1-159248476-A-C
• chr1-159248476-A-G
• chr1-159248476-A-T

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 0.561 in 152,068 control chromosomes in the GnomAD database, including 26,982 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 0.56 (26982 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 15 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.561 AC: 85181 AN: 151948 Hom.: 26933 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.561 AC: 85286 AN: 152068 Hom.: 26982 Cov.: 32 AF XY: 0.558 AC XY: 41494 AN XY: 74322

African (AFR) AF: 0.878 AC: 36459 AN: 41530

American (AMR) AF: 0.491 AC: 7499 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2852 AN: 5152

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4543 AN: 10548

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28367 AN: 67960

Other (OTH) AF: 0.517 AC: 1091 AN: 2110

Alfa AF: 0.454 Hom.: 72192

Bravo AF: 0.580

Asia WGS AF: 0.485 AC: 1687 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3845624; hg19: chr1-159218266;