rs4436440

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.776

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4436440; hg19: chr1-202052013;