rs7395920

Positions:

• chr11-1943082-T-C
• chr11-1943082-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.538

Alfa AF: 0.557 Hom.: 12451

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7395920; hg19: chr11-1964312;