rs1808279

Variant names:

• chr11-67444098-T-C
• rs1808279

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 0.523 in 150,238 control chromosomes in the GnomAD database, including 22,913 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 0.52 (22913 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.523 AC: 78456 AN: 150124 Hom.: 22880 Cov.: 26

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.523 AC: 78533 AN: 150238 Hom.: 22913 Cov.: 26 AF XY: 0.512 AC XY: 37509 AN XY: 73330

African (AFR) AF: 0.804 AC: 32929 AN: 40976

American (AMR) AF: 0.506 AC: 7646 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1112 AN: 3448

East Asian (EAS) AF: 0.296 AC: 1496 AN: 5060

South Asian (SAS) AF: 0.254 AC: 1208 AN: 4752

European-Finnish (FIN) AF: 0.372 AC: 3773 AN: 10152

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 28955 AN: 67476

Other (OTH) AF: 0.471 AC: 980 AN: 2080

Alfa AF: 0.490 Hom.: 2617

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.13
PhyloP100		-0.97
PromoterAI		-0.0054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1808279; hg19: chr11-67211569;