chr7-121314218-T-C

Variant names:

• chr7-121314218-T-C
• rs983926

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 0.949 in 152,248 control chromosomes in the GnomAD database, including 68,668 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 0.95 (68668 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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: 0.949 AC: 144344 AN: 152130 Hom.: 68607 Cov.: 31

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.949 AC: 144465 AN: 152248 Hom.: 68668 Cov.: 31 AF XY: 0.948 AC XY: 70553 AN XY: 74426

African (AFR) AF: 0.987 AC: 40997 AN: 41548

American (AMR) AF: 0.965 AC: 14762 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 3348 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5180

South Asian (SAS) AF: 0.989 AC: 4772 AN: 4826

European-Finnish (FIN) AF: 0.860 AC: 9093 AN: 10576

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63180 AN: 68030

Other (OTH) AF: 0.960 AC: 2024 AN: 2108

Alfa AF: 0.944 Hom.: 24631

Bravo AF: 0.958

Asia WGS AF: 0.993 AC: 3454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs983926; hg19: chr7-120954272;