11-4140326-T-C

Variant names:

• chr11-4140326-T-C
• rs4910896

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 0.876 in 152,158 control chromosomes in the GnomAD database, including 58,656 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 0.88 (58656 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.925 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: 0.876 AC: 133183 AN: 152040 Hom.: 58656 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.876 AC: 133218 AN: 152158 Hom.: 58656 Cov.: 31 AF XY: 0.871 AC XY: 64824 AN XY: 74402

African (AFR) AF: 0.797 AC: 33081 AN: 41488

American (AMR) AF: 0.853 AC: 13043 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3175 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3895 AN: 5180

South Asian (SAS) AF: 0.933 AC: 4493 AN: 4818

European-Finnish (FIN) AF: 0.885 AC: 9367 AN: 10580

Middle Eastern (MID) AF: 0.860 AC: 251 AN: 292

European-Non Finnish (NFE) AF: 0.931 AC: 63349 AN: 68026

Other (OTH) AF: 0.868 AC: 1834 AN: 2114

Alfa AF: 0.920 Hom.: 28045

Bravo AF: 0.868

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.25
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4910896; hg19: chr11-4161556;