11-71998226-C-T

Variant names:

• chr11-71998226-C-T
• rs3814721

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 0.831 in 151,888 control chromosomes in the GnomAD database, including 53,904 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 0.83 (53904 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 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: 0.831 AC: 126159 AN: 151770 Hom.: 53892 Cov.: 29

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.943

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.831 AC: 126212 AN: 151888 Hom.: 53904 Cov.: 29 AF XY: 0.829 AC XY: 61496 AN XY: 74216

African (AFR) AF: 0.622 AC: 25711 AN: 41346

American (AMR) AF: 0.807 AC: 12340 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3157 AN: 3468

East Asian (EAS) AF: 0.766 AC: 3921 AN: 5122

South Asian (SAS) AF: 0.840 AC: 4023 AN: 4790

European-Finnish (FIN) AF: 0.934 AC: 9885 AN: 10580

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64221 AN: 67984

Other (OTH) AF: 0.870 AC: 1834 AN: 2108

Alfa AF: 0.912 Hom.: 32175

Bravo AF: 0.815

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	14
DANN	Benign	0.62
PhyloP100		-0.19
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3814721; hg19: chr11-71709272;