7-130727469-C-T

Variant names:

• chr7-130727469-C-T
• rs4067229

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 0.393 in 151,942 control chromosomes in the GnomAD database, including 13,341 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 0.39 (13341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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: 0.394 AC: 59781 AN: 151822 Hom.: 13335 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.393 AC: 59786 AN: 151942 Hom.: 13341 Cov.: 32 AF XY: 0.394 AC XY: 29263 AN XY: 74242

African (AFR) AF: 0.173 AC: 7167 AN: 41468

American (AMR) AF: 0.448 AC: 6853 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3466

East Asian (EAS) AF: 0.553 AC: 2846 AN: 5148

South Asian (SAS) AF: 0.425 AC: 2052 AN: 4826

European-Finnish (FIN) AF: 0.491 AC: 5160 AN: 10510

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32628 AN: 67932

Other (OTH) AF: 0.408 AC: 859 AN: 2106

Alfa AF: 0.430 Hom.: 7382

Bravo AF: 0.384

Asia WGS AF: 0.461 AC: 1599 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.57
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4067229; hg19: chr7-130412296; COSMIC: COSV63294539;