11-75697172-T-C

Position:

• chr11-75697172-T-C

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 0.948 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.994

Gnomad4 OTH AF: 0.954

Alfa AF: 0.979 Hom.: 14501

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs487023; hg19: chr11-75408217;