7-38070256-C-A

Position:

• chr7-38070256-C-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 0.0577 in 152,144 control chromosomes in the GnomAD database, including 346 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 0.058 (346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 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: 0.0577 AC: 8772 AN: 152026 Hom.: 345 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0730

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

GnomAD4 genome AF: 0.0577 AC: 8774 AN: 152144 Hom.: 346 Cov.: 32 AF XY: 0.0593 AC XY: 4409 AN XY: 74372

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0485

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.0727

Alfa AF: 0.0656 Hom.: 65

Bravo AF: 0.0543

Asia WGS AF: 0.0990 AC: 345 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9648058; hg19: chr7-38109858;