7-42389030-G-A

Position:

• chr7-42389030-G-A

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 0.0536 in 152,228 control chromosomes in the GnomAD database, including 277 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 0.054 (277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0946 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: 0.0537 AC: 8164 AN: 152110 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0754

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0536 AC: 8161 AN: 152228 Hom.: 277 Cov.: 32 AF XY: 0.0550 AC XY: 4097 AN XY: 74430

Gnomad4 AFR AF: 0.0185

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.0147

Gnomad4 FIN AF: 0.0754

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0636 Hom.: 62

Bravo AF: 0.0553

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12531052; hg19: chr7-42428629;