7-114715042-A-G

Variant names:

• chr7-114715042-A-G
• rs1378769

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.382 AC: 15828 AN: 41450

American (AMR) AF: 0.136 AC: 2081 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3470

East Asian (EAS) AF: 0.350 AC: 1807 AN: 5158

South Asian (SAS) AF: 0.124 AC: 598 AN: 4820

European-Finnish (FIN) AF: 0.0289 AC: 307 AN: 10610

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.0434 AC: 2952 AN: 67990

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.0857 Hom.: 5976

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
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1378769; hg19: chr7-114355097;