rs10484596

Variant names:

• chr6-137410807-A-G
• rs10484596

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 0.0635 in 152,260 control chromosomes in the GnomAD database, including 670 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 0.063 (670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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: 0.0633 AC: 9627 AN: 152142 Hom.: 665 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0304

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0416

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0611

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

GnomAD4 genome AF: 0.0635 AC: 9662 AN: 152260 Hom.: 670 Cov.: 32 AF XY: 0.0618 AC XY: 4604 AN XY: 74454

African (AFR) AF: 0.173 AC: 7188 AN: 41522

American (AMR) AF: 0.0304 AC: 464 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4822

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10618

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1392 AN: 68030

Other (OTH) AF: 0.0605 AC: 128 AN: 2116

Alfa AF: 0.0411 Hom.: 509

Bravo AF: 0.0700

Asia WGS AF: 0.0240 AC: 86 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.9
DANN	Benign	0.59
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10484596; hg19: chr6-137731944;