11-1943082-T-C

Variant names:

• chr11-1943082-T-C
• rs7395920

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 0.532 in 152,030 control chromosomes in the GnomAD database, including 22,057 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 0.53 (22057 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.75
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 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: 0.533 AC: 80918 AN: 151912 Hom.: 22052 Cov.: 34

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.532 AC: 80950 AN: 152030 Hom.: 22057 Cov.: 34 AF XY: 0.529 AC XY: 39297 AN XY: 74334

African (AFR) AF: 0.462 AC: 19169 AN: 41454

American (AMR) AF: 0.392 AC: 5986 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3468

East Asian (EAS) AF: 0.602 AC: 3110 AN: 5162

South Asian (SAS) AF: 0.475 AC: 2293 AN: 4828

European-Finnish (FIN) AF: 0.603 AC: 6379 AN: 10576

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40360 AN: 67950

Other (OTH) AF: 0.538 AC: 1133 AN: 2104

Alfa AF: 0.566 Hom.: 19079

Bravo AF: 0.514

Asia WGS AF: 0.496 AC: 1723 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.098
PhyloP100		-4.7

Splicing

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

Other links and lift over

dbSNP: rs7395920; hg19: chr11-1964312;