chr7-41582932-G-T

Position:

• chr7-41582932-G-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 0.931 in 152,262 control chromosomes in the GnomAD database, including 66,179 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 0.93 (66179 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.961 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: 0.931 AC: 141697 AN: 152144 Hom.: 66154 Cov.: 33

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.958

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.931 AC: 141771 AN: 152262 Hom.: 66179 Cov.: 33 AF XY: 0.930 AC XY: 69228 AN XY: 74454

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.958

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.968

Gnomad4 OTH AF: 0.937

Alfa AF: 0.954 Hom.: 32862

Bravo AF: 0.923

Asia WGS AF: 0.893 AC: 3105 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4724055; hg19: chr7-41622530;