11-67577193-C-T

Variant names:

• chr11-67577193-C-T
• rs625978

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 0.401 in 151,850 control chromosomes in the GnomAD database, including 14,428 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 0.40 (14428 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.401 AC: 60862 AN: 151732 Hom.: 14430 Cov.: 30

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.401 AC: 60870 AN: 151850 Hom.: 14428 Cov.: 30 AF XY: 0.412 AC XY: 30568 AN XY: 74214

African (AFR) AF: 0.144 AC: 5953 AN: 41440

American (AMR) AF: 0.399 AC: 6088 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2223 AN: 3464

East Asian (EAS) AF: 0.684 AC: 3504 AN: 5122

South Asian (SAS) AF: 0.623 AC: 2991 AN: 4800

European-Finnish (FIN) AF: 0.517 AC: 5468 AN: 10568

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33049 AN: 67896

Other (OTH) AF: 0.444 AC: 934 AN: 2104

Alfa AF: 0.387 Hom.: 1987

Bravo AF: 0.379

Asia WGS AF: 0.602 AC: 2092 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.7
DANN	Benign	0.84
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs625978; hg19: chr11-67344664;