11-75697172-T-C

Variant names:

• chr11-75697172-T-C
• rs487023

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 0.948 in 152,262 control chromosomes in the GnomAD database, including 68,870 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 (68870 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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: 0.948 AC: 144181 AN: 152144 Hom.: 68819 Cov.: 33

Gnomad AFR AF: 0.959

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.948 AC: 144290 AN: 152262 Hom.: 68870 Cov.: 33 AF XY: 0.938 AC XY: 69842 AN XY: 74436

African (AFR) AF: 0.959 AC: 39865 AN: 41576

American (AMR) AF: 0.859 AC: 13138 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3446 AN: 3472

East Asian (EAS) AF: 0.612 AC: 3156 AN: 5158

South Asian (SAS) AF: 0.913 AC: 4407 AN: 4826

European-Finnish (FIN) AF: 0.891 AC: 9416 AN: 10570

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

European-Non Finnish (NFE) AF: 0.994 AC: 67641 AN: 68038

Other (OTH) AF: 0.954 AC: 2019 AN: 2116

Alfa AF: 0.979 Hom.: 24620

Bravo AF: 0.944

Asia WGS AF: 0.792 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs487023; hg19: chr11-75408217;