7-42345021-T-C

Variant names:

• chr7-42345021-T-C
• rs7791745

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 0.733 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.717 AC: 29758 AN: 41490

American (AMR) AF: 0.816 AC: 12478 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2706 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3346 AN: 5152

South Asian (SAS) AF: 0.674 AC: 3243 AN: 4810

European-Finnish (FIN) AF: 0.605 AC: 6380 AN: 10546

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51187 AN: 67970

Other (OTH) AF: 0.744 AC: 1572 AN: 2112

Alfa AF: 0.751 Hom.: 191417

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7791745; hg19: chr7-42384620;