7-132000004-A-G

Variant names:

• chr7-132000004-A-G
• rs6467411

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 0.879 in 152,232 control chromosomes in the GnomAD database, including 59,140 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 0.88 (59140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 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: 0.879 AC: 133697 AN: 152114 Hom.: 59074 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.834

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.879 AC: 133826 AN: 152232 Hom.: 59140 Cov.: 32 AF XY: 0.880 AC XY: 65477 AN XY: 74404

African (AFR) AF: 0.958 AC: 39813 AN: 41560

American (AMR) AF: 0.886 AC: 13538 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5076 AN: 5160

South Asian (SAS) AF: 0.908 AC: 4384 AN: 4826

European-Finnish (FIN) AF: 0.848 AC: 8987 AN: 10600

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.831 AC: 56522 AN: 68014

Other (OTH) AF: 0.860 AC: 1818 AN: 2114

Alfa AF: 0.870 Hom.: 10305

Bravo AF: 0.885

Asia WGS AF: 0.942 AC: 3272 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs6467411; hg19: chr7-131684763;