chr10-5998631-G-A

Variant names:

• chr10-5998631-G-A
• rs7477011

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 0.403 in 151,268 control chromosomes in the GnomAD database, including 13,357 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 0.40 (13357 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 8 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 (NFE) allele frequency at 95% confidence interval = 0.492 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: 0.403 AC: 60934 AN: 151158 Hom.: 13351 Cov.: 29

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.387

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.403 AC: 60972 AN: 151268 Hom.: 13357 Cov.: 29 AF XY: 0.398 AC XY: 29425 AN XY: 73866

African (AFR) AF: 0.250 AC: 10301 AN: 41206

American (AMR) AF: 0.377 AC: 5729 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1657 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5168

South Asian (SAS) AF: 0.404 AC: 1931 AN: 4782

European-Finnish (FIN) AF: 0.393 AC: 4048 AN: 10300

Middle Eastern (MID) AF: 0.385 AC: 111 AN: 288

European-Non Finnish (NFE) AF: 0.497 AC: 33711 AN: 67852

Other (OTH) AF: 0.408 AC: 856 AN: 2096

Alfa AF: 0.347 Hom.: 1517

Bravo AF: 0.392

Asia WGS AF: 0.437 AC: 1519 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	2.2
DANN	Benign	0.54
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs7477011; hg19: chr10-6040594;