rs10238549

Variant names:

• chr7-110540965-C-T
• rs10238549

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 0.272 in 151,884 control chromosomes in the GnomAD database, including 5,735 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 0.27 (5735 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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: 0.272 AC: 41255 AN: 151764 Hom.: 5728 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.272 AC: 41272 AN: 151884 Hom.: 5735 Cov.: 31 AF XY: 0.270 AC XY: 20078 AN XY: 74248

African (AFR) AF: 0.239 AC: 9925 AN: 41452

American (AMR) AF: 0.288 AC: 4390 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1183 AN: 3464

East Asian (EAS) AF: 0.138 AC: 714 AN: 5158

South Asian (SAS) AF: 0.203 AC: 976 AN: 4814

European-Finnish (FIN) AF: 0.313 AC: 3304 AN: 10562

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19785 AN: 67894

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.284 Hom.: 19394

Bravo AF: 0.268

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.45
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10238549; hg19: chr7-110181022;