rs1948368

Positions:

• chr1-101472921-G-A
• chr1-101472921-G-C

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 0.533 in 151,772 control chromosomes in the GnomAD database, including 21,877 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 0.53 (21877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.534 AC: 80910 AN: 151654 Hom.: 21868 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.533 AC: 80956 AN: 151772 Hom.: 21877 Cov.: 32 AF XY: 0.532 AC XY: 39441 AN XY: 74170

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.523

Alfa AF: 0.501 Hom.: 35735

Bravo AF: 0.534

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1948368; hg19: chr1-101938477;