rs4387163

Variant names:

• chr1-165026476-G-A
• rs4387163

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 0.449 in 152,022 control chromosomes in the GnomAD database, including 19,174 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 0.45 (19174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 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: 0.450 AC: 68296 AN: 151904 Hom.: 19181 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.449 AC: 68276 AN: 152022 Hom.: 19174 Cov.: 32 AF XY: 0.450 AC XY: 33462 AN XY: 74300

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.476

Alfa AF: 0.582 Hom.: 56595

Bravo AF: 0.414

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4387163; hg19: chr1-164995713;