rs1255149

Variant names:

• chr11-95751330-A-G
• rs1255149

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 0.941 in 152,272 control chromosomes in the GnomAD database, including 67,638 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 0.94 (67638 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 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: 0.941 AC: 143232 AN: 152154 Hom.: 67586 Cov.: 31

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.941 AC: 143346 AN: 152272 Hom.: 67638 Cov.: 31 AF XY: 0.938 AC XY: 69821 AN XY: 74444

African (AFR) AF: 0.964 AC: 40065 AN: 41552

American (AMR) AF: 0.924 AC: 14150 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3272 AN: 3472

East Asian (EAS) AF: 0.715 AC: 3696 AN: 5166

South Asian (SAS) AF: 0.874 AC: 4211 AN: 4820

European-Finnish (FIN) AF: 0.927 AC: 9830 AN: 10608

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.956 AC: 65013 AN: 68034

Other (OTH) AF: 0.932 AC: 1962 AN: 2106

Alfa AF: 0.947 Hom.: 11844

Bravo AF: 0.941

Asia WGS AF: 0.830 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.9
DANN	Benign	0.30
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1255149; hg19: chr11-95484494;