rs7905355

Variant names:

• chr10-124236026-A-G
• rs7905355

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 0.336 in 152,008 control chromosomes in the GnomAD database, including 9,003 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 0.34 (9003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.336 AC: 51076 AN: 151890 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.336 AC: 51121 AN: 152008 Hom.: 9003 Cov.: 32 AF XY: 0.340 AC XY: 25274 AN XY: 74290

African (AFR) AF: 0.269 AC: 11158 AN: 41450

American (AMR) AF: 0.350 AC: 5344 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3468

East Asian (EAS) AF: 0.604 AC: 3120 AN: 5162

South Asian (SAS) AF: 0.336 AC: 1620 AN: 4820

European-Finnish (FIN) AF: 0.382 AC: 4031 AN: 10546

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23491 AN: 67968

Other (OTH) AF: 0.330 AC: 696 AN: 2106

Alfa AF: 0.344 Hom.: 29739

Bravo AF: 0.332

Asia WGS AF: 0.498 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.34
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7905355; hg19: chr10-125924595;