rs613804

Positions:

• chr11-102849690-G-A

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 0.0967 in 152,146 control chromosomes in the GnomAD database, including 976 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 0.097 (976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14705 AN: 152028 Hom.: 972 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0967 AC: 14711 AN: 152146 Hom.: 976 Cov.: 32 AF XY: 0.0951 AC XY: 7075 AN XY: 74374

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.0942

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0645 Hom.: 315

Bravo AF: 0.103

Asia WGS AF: 0.109 AC: 379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs613804; hg19: chr11-102720421;