rs10484965

Variant names:

• chr6-119923639-G-A
• rs10484965

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 0.163 in 152,184 control chromosomes in the GnomAD database, including 2,208 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 0.16 (2208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24764 AN: 152066 Hom.: 2208 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.163 AC: 24771 AN: 152184 Hom.: 2208 Cov.: 32 AF XY: 0.160 AC XY: 11895 AN XY: 74408

African (AFR) AF: 0.205 AC: 8513 AN: 41516

American (AMR) AF: 0.109 AC: 1666 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.165 AC: 795 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1465 AN: 10594

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.165 AC: 11236 AN: 67990

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.165 Hom.: 7103

Bravo AF: 0.162

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.4
DANN	Benign	0.82
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10484965; hg19: chr6-120244785; COSMIC: COSV69423040;