chr7-116196743-T-C

Variant names:

• chr7-116196743-T-C
• rs2402053

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 0.457 in 151,968 control chromosomes in the GnomAD database, including 16,376 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 0.46 (16376 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.457 AC: 69328 AN: 151850 Hom.: 16362 Cov.: 31

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.457 AC: 69384 AN: 151968 Hom.: 16376 Cov.: 31 AF XY: 0.461 AC XY: 34212 AN XY: 74264

African (AFR) AF: 0.525 AC: 21772 AN: 41456

American (AMR) AF: 0.411 AC: 6275 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3464

East Asian (EAS) AF: 0.793 AC: 4088 AN: 5154

South Asian (SAS) AF: 0.462 AC: 2223 AN: 4810

European-Finnish (FIN) AF: 0.463 AC: 4896 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.402 AC: 27311 AN: 67930

Other (OTH) AF: 0.459 AC: 969 AN: 2112

Alfa AF: 0.420 Hom.: 9531

Bravo AF: 0.458

Asia WGS AF: 0.648 AC: 2251 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	0.89
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2402053; hg19: chr7-115836797;