rs1277718

Variant names:

• chr11-102876821-G-C
• rs1277718

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 0.135 in 152,174 control chromosomes in the GnomAD database, including 2,443 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 0.14 (2443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.318 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: 0.135 AC: 20597 AN: 152056 Hom.: 2436 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.135 AC: 20617 AN: 152174 Hom.: 2443 Cov.: 32 AF XY: 0.133 AC XY: 9882 AN XY: 74414

African (AFR) AF: 0.323 AC: 13377 AN: 41464

American (AMR) AF: 0.0843 AC: 1289 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.109 AC: 563 AN: 5182

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4824

European-Finnish (FIN) AF: 0.0406 AC: 431 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0535 AC: 3638 AN: 68010

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.104 Hom.: 211

Bravo AF: 0.147

Asia WGS AF: 0.115 AC: 401 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	0.92
DANN	Benign	0.75
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1277718; hg19: chr11-102747551;