7-128104735-T-C

Variant names:

• chr7-128104735-T-C
• rs322812

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 0.473 in 151,914 control chromosomes in the GnomAD database, including 17,610 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 0.47 (17610 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.474 AC: 71877 AN: 151796 Hom.: 17593 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.473 AC: 71927 AN: 151914 Hom.: 17610 Cov.: 31 AF XY: 0.465 AC XY: 34509 AN XY: 74228

African (AFR) AF: 0.573 AC: 23733 AN: 41396

American (AMR) AF: 0.484 AC: 7394 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3470

East Asian (EAS) AF: 0.152 AC: 790 AN: 5182

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4820

European-Finnish (FIN) AF: 0.395 AC: 4159 AN: 10528

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30946 AN: 67938

Other (OTH) AF: 0.460 AC: 968 AN: 2104

Alfa AF: 0.459 Hom.: 51632

Bravo AF: 0.488

Asia WGS AF: 0.260 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.64
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs322812; hg19: chr7-127744787;