rs10493643

Variant names:

• chr1-79887054-G-A
• rs10493643

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 0.0722 in 151,890 control chromosomes in the GnomAD database, including 497 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 0.072 (497 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.0722 AC: 10958 AN: 151772 Hom.: 495 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0722 AC: 10966 AN: 151890 Hom.: 497 Cov.: 33 AF XY: 0.0722 AC XY: 5359 AN XY: 74196

African (AFR) AF: 0.116 AC: 4799 AN: 41428

American (AMR) AF: 0.0461 AC: 705 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3468

East Asian (EAS) AF: 0.0366 AC: 189 AN: 5166

South Asian (SAS) AF: 0.154 AC: 741 AN: 4820

European-Finnish (FIN) AF: 0.0288 AC: 302 AN: 10484

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0550 AC: 3735 AN: 67928

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0655 Hom.: 206

Bravo AF: 0.0729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.10
DANN	Benign	0.23
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10493643; hg19: chr1-80352739;