rs1939214

Variant names:

• chr11-124735394-A-G
• rs1939214
• ENST00000844206.1:n.180-4518A>G

Variant summary

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

The ENST00000844206.1(ENSG00000309835):​n.180-4518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,132 control chromosomes in the GnomAD database, including 2,621 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 0.18 (2621 hom., cov: 32)
• Consequence: ENSG00000309835 ENST00000844206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 8 publications found

Genes affected

ENSG00000309835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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
ENSG00000309835	ENST00000844206.1	n.180-4518A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27407 AN: 152012 Hom.: 2608 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.181 AC: 27471 AN: 152132 Hom.: 2621 Cov.: 32 AF XY: 0.177 AC XY: 13147 AN XY: 74388

African (AFR) AF: 0.237 AC: 9829 AN: 41474

American (AMR) AF: 0.119 AC: 1814 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1080 AN: 5182

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1713 AN: 10586

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11449 AN: 68004

Other (OTH) AF: 0.182 AC: 384 AN: 2110

Alfa AF: 0.169 Hom.: 8909

Bravo AF: 0.181

Asia WGS AF: 0.198 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.78
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1939214; hg19: chr11-124605290; COSMIC: COSV107315854;