chr7-41386301-A-C

Position:

• chr7-41386301-A-C

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 0.653 in 151,790 control chromosomes in the GnomAD database, including 33,199 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 0.65 (33199 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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 = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98952 AN: 151672 Hom.: 33148 Cov.: 30

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.653 AC: 99062 AN: 151790 Hom.: 33199 Cov.: 30 AF XY: 0.650 AC XY: 48213 AN XY: 74144

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.640

Alfa AF: 0.453 Hom.: 1081

Bravo AF: 0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs273098; hg19: chr7-41425899;