rs3808969

Variant names:

• chr11-68005259-A-G
• rs3808969
• ENST00000840917.1:n.108A>G

Variant summary

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

The ENST00000840917.1(ENSG00000309414):​n.108A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,208 control chromosomes in the GnomAD database, including 1,981 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 0.16 (1981 hom., cov: 33)
• Consequence: ENSG00000309414 ENST00000840917.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 11 publications found

Genes affected

ENSG00000309414 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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
ENSG00000309414	ENST00000840917.1	n.108A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000309414	ENST00000840914.1	n.168-1182A>G		intron_variant	Intron 1 of 1
ENSG00000309414	ENST00000840915.1	n.526-1182A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23638 AN: 152090 Hom.: 1979 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.155 AC: 23648 AN: 152208 Hom.: 1981 Cov.: 33 AF XY: 0.155 AC XY: 11555 AN XY: 74408

African (AFR) AF: 0.103 AC: 4269 AN: 41552

American (AMR) AF: 0.149 AC: 2278 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 629 AN: 3460

East Asian (EAS) AF: 0.182 AC: 946 AN: 5184

South Asian (SAS) AF: 0.171 AC: 826 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1926 AN: 10582

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12115 AN: 67998

Other (OTH) AF: 0.151 AC: 319 AN: 2112

Alfa AF: 0.168 Hom.: 3721

Bravo AF: 0.151

Asia WGS AF: 0.156 AC: 542 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		-0.72
PromoterAI		0.057	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3808969; hg19: chr11-67772729;