rs7895441

Positions:

• chr10-95580173-G-A

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 0.253 in 152,070 control chromosomes in the GnomAD database, including 5,645 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 0.25 (5645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38485 AN: 151952 Hom.: 5645 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.253 AC: 38511 AN: 152070 Hom.: 5645 Cov.: 32 AF XY: 0.250 AC XY: 18607 AN XY: 74324

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.279

Alfa AF: 0.213 Hom.: 7477

Bravo AF: 0.262

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.35
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7895441; hg19: chr10-97339930;