chr7-121635175-C-T

Variant names:

• chr7-121635175-C-T
• rs10253361

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 0.621 in 152,008 control chromosomes in the GnomAD database, including 30,255 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 0.62 (30255 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.620 AC: 94201 AN: 151888 Hom.: 30205 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.621 AC: 94322 AN: 152008 Hom.: 30255 Cov.: 32 AF XY: 0.619 AC XY: 45989 AN XY: 74248

African (AFR) AF: 0.778 AC: 32275 AN: 41480

American (AMR) AF: 0.533 AC: 8130 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2017 AN: 5158

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4814

European-Finnish (FIN) AF: 0.684 AC: 7214 AN: 10544

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38375 AN: 67960

Other (OTH) AF: 0.599 AC: 1266 AN: 2114

Alfa AF: 0.571 Hom.: 113236

Bravo AF: 0.614

Asia WGS AF: 0.528 AC: 1839 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.18
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10253361; hg19: chr7-121275229;