rs1948368

Variant names:

• chr1-101472921-G-A
• rs1948368

Your query was ambiguous. Multiple possible variants found:

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

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 0.533 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.609 AC: 25197 AN: 41376

American (AMR) AF: 0.497 AC: 7588 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1656 AN: 5156

South Asian (SAS) AF: 0.490 AC: 2354 AN: 4802

European-Finnish (FIN) AF: 0.554 AC: 5820 AN: 10508

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34585 AN: 67884

Other (OTH) AF: 0.523 AC: 1100 AN: 2102

Alfa AF: 0.512 Hom.: 62082

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
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs1948368; hg19: chr1-101938477;