rs4970605

chr1-38581447-G-Achr1-38581447-G-Cchr1-38581447-G-T

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 0.742 in 152,048 control chromosomes in the GnomAD database, including 42,581 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 0.74 (42581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112796 AN: 151930 Hom.: 42550 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.742 AC: 112879 AN: 152048 Hom.: 42581 Cov.: 32 AF XY: 0.746 AC XY: 55430 AN XY: 74304

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.744

Alfa AF: 0.763 Hom.: 41449

Bravo AF: 0.734

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.10
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: rs4970605; hg19: chr1-39047119;