rs4436440

Variant names:

• chr1-202082885-T-A
• rs4436440

Your query was ambiguous. Multiple possible variants found:

• chr1-202082885-T-A
• chr1-202082885-T-G

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 0.791 in 151,858 control chromosomes in the GnomAD database, including 48,208 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 0.79 (48208 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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: 0.791 AC: 120089 AN: 151740 Hom.: 48160 Cov.: 30

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.791 AC: 120189 AN: 151858 Hom.: 48208 Cov.: 30 AF XY: 0.792 AC XY: 58818 AN XY: 74232

African (AFR) AF: 0.924 AC: 38311 AN: 41462

American (AMR) AF: 0.805 AC: 12289 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2767 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3160 AN: 5098

South Asian (SAS) AF: 0.787 AC: 3777 AN: 4800

European-Finnish (FIN) AF: 0.731 AC: 7700 AN: 10536

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49626 AN: 67922

Other (OTH) AF: 0.776 AC: 1635 AN: 2108

Alfa AF: 0.767 Hom.: 5611

Bravo AF: 0.802

Asia WGS AF: 0.715 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.46
DANN	Benign	0.58
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4436440; hg19: chr1-202052013;