rs10238549

Positions:

• chr7-110540965-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.297

Alfa AF: 0.288 Hom.: 12999

Bravo AF: 0.268

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10238549; hg19: chr7-110181022;