rs7104908

Variant names:

• chr11-76256419-G-A
• rs7104908

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.503 in 141,790 control chromosomes in the GnomAD database, including 18,605 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 0.50 (18605 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 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: 0.504 AC: 71386 AN: 141700 Hom.: 18611 Cov.: 24

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.503 AC: 71381 AN: 141790 Hom.: 18605 Cov.: 24 AF XY: 0.496 AC XY: 34078 AN XY: 68678

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.534

Alfa AF: 0.527 Hom.: 2398

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7104908; hg19: chr11-75967463;