7-42388861-A-C

Position:

• chr7-42388861-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 0.0537 in 152,264 control chromosomes in the GnomAD database, including 281 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 (281 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0949 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: 0.0538 AC: 8185 AN: 152146 Hom.: 282 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0757

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: 0.0537 AC: 8182 AN: 152264 Hom.: 281 Cov.: 32 AF XY: 0.0552 AC XY: 4112 AN XY: 74454

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.0217

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0634 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	-0.98
CADD	Benign	2.3
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12536071; hg19: chr7-42428460;