7-107725406-C-T

Variant names:

• chr7-107725406-C-T
• rs11972418

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 0.434 in 152,084 control chromosomes in the GnomAD database, including 14,483 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 0.43 (14483 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.434 AC: 65961 AN: 151968 Hom.: 14495 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.434 AC: 65967 AN: 152084 Hom.: 14483 Cov.: 33 AF XY: 0.435 AC XY: 32338 AN XY: 74338

African (AFR) AF: 0.392 AC: 16246 AN: 41492

American (AMR) AF: 0.436 AC: 6669 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3241 AN: 5168

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4927 AN: 10566

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29900 AN: 67966

Other (OTH) AF: 0.432 AC: 914 AN: 2116

Alfa AF: 0.429 Hom.: 1771

Bravo AF: 0.434

Asia WGS AF: 0.484 AC: 1688 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	1.3
DANN	Benign	0.77
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs11972418; hg19: chr7-107365851;