chr7-121635175-C-T

Position:

• chr7-121635175-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 0.621 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.599

Alfa AF: 0.559 Hom.: 55970

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10253361; hg19: chr7-121275229;