rs7128311

Variant names:

• chr11-20540973-C-T
• rs7128311

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 0.969 in 152,312 control chromosomes in the GnomAD database, including 72,006 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 0.97 (72006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.970 AC: 147556 AN: 152194 Hom.: 71957 Cov.: 32

Gnomad AFR AF: 0.994

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.969 AC: 147663 AN: 152312 Hom.: 72006 Cov.: 32 AF XY: 0.966 AC XY: 71945 AN XY: 74470

African (AFR) AF: 0.994 AC: 41330 AN: 41572

American (AMR) AF: 0.898 AC: 13741 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3429 AN: 3472

East Asian (EAS) AF: 0.628 AC: 3242 AN: 5162

South Asian (SAS) AF: 0.966 AC: 4658 AN: 4824

European-Finnish (FIN) AF: 0.975 AC: 10352 AN: 10620

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.995 AC: 67669 AN: 68042

Other (OTH) AF: 0.965 AC: 2038 AN: 2112

Alfa AF: 0.973 Hom.: 143037

Bravo AF: 0.959

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.58
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7128311; hg19: chr11-20562519;