rs949083

Variant names:

• chr11-79634818-T-C
• rs949083
• ENST00000789891.1:n.65-7403A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-79634818-T-C
• chr11-79634818-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789891.1(ENSG00000302828):​n.65-7403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,092 control chromosomes in the GnomAD database, including 9,868 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 0.35 (9868 hom., cov: 33)
• Consequence: ENSG00000302828 ENST00000789891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 6 publications found

Genes affected

ENSG00000302828 (HGNC:):

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 = 0.431 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
ENSG00000302828	ENST00000789891.1	n.65-7403A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53390 AN: 151974 Hom.: 9872 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.351 AC: 53398 AN: 152092 Hom.: 9868 Cov.: 33 AF XY: 0.347 AC XY: 25779 AN XY: 74380

African (AFR) AF: 0.437 AC: 18093 AN: 41438

American (AMR) AF: 0.291 AC: 4453 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3466

East Asian (EAS) AF: 0.0963 AC: 499 AN: 5180

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2404 AN: 10592

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23357 AN: 67986

Other (OTH) AF: 0.363 AC: 767 AN: 2114

Alfa AF: 0.354 Hom.: 16471

Bravo AF: 0.355

Asia WGS AF: 0.258 AC: 898 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	0.21
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs949083; hg19: chr11-79345862;