7-42345021-T-C

Variant names:

• chr7-42345021-T-C
• rs7791745

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 0.733 in 152,050 control chromosomes in the GnomAD database, including 41,120 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 0.73 (41120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 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: 0.734 AC: 111455 AN: 151932 Hom.: 41088 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.733 AC: 111528 AN: 152050 Hom.: 41120 Cov.: 32 AF XY: 0.728 AC XY: 54101 AN XY: 74314

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.744

Alfa AF: 0.754 Hom.: 90563

Bravo AF: 0.750

Asia WGS AF: 0.642 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7791745; hg19: chr7-42384620;