7-141033894-A-G

Variant names:

• chr7-141033894-A-G
• rs1068266

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 0.131 in 151,164 control chromosomes in the GnomAD database, including 1,402 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 0.13 (1402 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.131 AC: 19855 AN: 151048 Hom.: 1400 Cov.: 29

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.131 AC: 19870 AN: 151164 Hom.: 1402 Cov.: 29 AF XY: 0.126 AC XY: 9333 AN XY: 73816

African (AFR) AF: 0.151 AC: 6210 AN: 41108

American (AMR) AF: 0.0850 AC: 1291 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 455 AN: 3454

East Asian (EAS) AF: 0.00599 AC: 31 AN: 5172

South Asian (SAS) AF: 0.0968 AC: 460 AN: 4752

European-Finnish (FIN) AF: 0.108 AC: 1127 AN: 10462

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9813 AN: 67720

Other (OTH) AF: 0.123 AC: 259 AN: 2100

Alfa AF: 0.0600 Hom.: 71

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.27
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1068266; hg19: chr7-140733694;