11-18998417-T-C

Variant names:

• chr11-18998417-T-C
• rs1601043

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 0.894 in 152,154 control chromosomes in the GnomAD database, including 62,485 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 0.89 (62485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135927 AN: 152036 Hom.: 62443 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.894 AC: 136026 AN: 152154 Hom.: 62485 Cov.: 32 AF XY: 0.899 AC XY: 66859 AN XY: 74388

African (AFR) AF: 0.654 AC: 27123 AN: 41460

American (AMR) AF: 0.960 AC: 14673 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 3386 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5151 AN: 5168

South Asian (SAS) AF: 0.996 AC: 4808 AN: 4826

European-Finnish (FIN) AF: 0.995 AC: 10565 AN: 10616

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67168 AN: 68004

Other (OTH) AF: 0.925 AC: 1955 AN: 2114

Alfa AF: 0.941 Hom.: 28878

Bravo AF: 0.880

Asia WGS AF: 0.970 AC: 3372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Other links and lift over

dbSNP: rs1601043; hg19: chr11-19019964;