rs1385397

Variant names:

• chr14-87290134-G-C
• rs1385397
• ENST00000849835.1:n.97-15981G>C

Variant summary

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

The ENST00000849835.1(ENSG00000310449):​n.97-15981G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,952 control chromosomes in the GnomAD database, including 14,119 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 0.42 (14119 hom., cov: 32)
• Consequence: ENSG00000310449 ENST00000849835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 0 publications found

Genes affected

ENSG00000310449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 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
ENSG00000310449	ENST00000849835.1	n.97-15981G>C		intron_variant	Intron 1 of 3
ENSG00000310462	ENST00000850009.1	n.35-508C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63338 AN: 151834 Hom.: 14113 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.417 AC: 63354 AN: 151952 Hom.: 14119 Cov.: 32 AF XY: 0.419 AC XY: 31138 AN XY: 74266

African (AFR) AF: 0.251 AC: 10411 AN: 41460

American (AMR) AF: 0.437 AC: 6673 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1777 AN: 5152

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4826

European-Finnish (FIN) AF: 0.520 AC: 5479 AN: 10538

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34053 AN: 67930

Other (OTH) AF: 0.419 AC: 884 AN: 2108

Alfa AF: 0.451 Hom.: 1978

Bravo AF: 0.407

Asia WGS AF: 0.319 AC: 1105 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.57
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1385397; hg19: chr14-87756478;