11-56698623-C-T

Variant names:

• chr11-56698623-C-T
• rs1397048

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.53 in 134,264 control chromosomes in the GnomAD database, including 17,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.53 (17767 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.67
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 11-56698623-C-T is Benign according to our data. Variant chr11-56698623-C-T is described in ClinVar as Benign. ClinVar VariationId is 873251.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.530 AC: 71053 AN: 134154 Hom.: 17727 Cov.: 35

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.530 AC: 71131 AN: 134264 Hom.: 17767 Cov.: 35 AF XY: 0.526 AC XY: 34394 AN XY: 65430

African (AFR) AF: 0.708 AC: 28334 AN: 40026

American (AMR) AF: 0.396 AC: 5129 AN: 12954

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1368 AN: 2908

East Asian (EAS) AF: 0.331 AC: 1343 AN: 4062

South Asian (SAS) AF: 0.364 AC: 1467 AN: 4026

European-Finnish (FIN) AF: 0.494 AC: 4568 AN: 9256

Middle Eastern (MID) AF: 0.478 AC: 128 AN: 268

European-Non Finnish (NFE) AF: 0.474 AC: 27569 AN: 58154

Other (OTH) AF: 0.486 AC: 918 AN: 1888

Alfa AF: 0.411 Hom.: 57676

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.053
DANN	Benign	0.21
PhyloP100		-1.7
PromoterAI		-0.0041	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1397048; hg19: chr11-56466099; COSMIC: COSV56450500;