chr7-114715042-A-G

Position:

• chr7-114715042-A-G

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 0.161 in 152,110 control chromosomes in the GnomAD database, including 3,673 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 0.16 (3673 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.114715042A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24415 AN: 151992 Hom.: 3668 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0289

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.161 AC: 24457 AN: 152110 Hom.: 3673 Cov.: 32 AF XY: 0.161 AC XY: 11999 AN XY: 74392

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0289

Gnomad4 NFE AF: 0.0434

Gnomad4 OTH AF: 0.164

Alfa AF: 0.0700 Hom.: 1587

Bravo AF: 0.180

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378769; hg19: chr7-114355097;