chr7-128927756-C-T

Variant names:

• chr7-128927756-C-T
• rs13245639

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 0.279 in 151,962 control chromosomes in the GnomAD database, including 6,363 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 0.28 (6363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.321 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: 0.279 AC: 42357 AN: 151844 Hom.: 6361 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.279 AC: 42376 AN: 151962 Hom.: 6363 Cov.: 32 AF XY: 0.281 AC XY: 20893 AN XY: 74266

African (AFR) AF: 0.198 AC: 8211 AN: 41442

American (AMR) AF: 0.216 AC: 3299 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1640 AN: 5152

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4812

European-Finnish (FIN) AF: 0.351 AC: 3703 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22075 AN: 67936

Other (OTH) AF: 0.253 AC: 535 AN: 2112

Alfa AF: 0.286 Hom.: 829

Bravo AF: 0.265

Asia WGS AF: 0.307 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs13245639; hg19: chr7-128567810;