chr7-113094238-G-A

Position:

• chr7-113094238-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 0.0562 in 151,972 control chromosomes in the GnomAD database, including 297 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 0.056 (297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.123 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: 0.0562 AC: 8532 AN: 151854 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0595

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.0494

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

GnomAD4 genome AF: 0.0562 AC: 8536 AN: 151972 Hom.: 297 Cov.: 32 AF XY: 0.0579 AC XY: 4304 AN XY: 74288

Gnomad4 AFR AF: 0.0272

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0595

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0699

Gnomad4 OTH AF: 0.0489

Alfa AF: 0.0648 Hom.: 60

Bravo AF: 0.0503

Asia WGS AF: 0.0850 AC: 296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7778565; hg19: chr7-112734293;