rs1210840

Variant names:

• chr14-81976050-G-A
• rs1210840
• ENST00000554814.1:n.316-54056G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-81976050-G-A
• chr14-81976050-G-T

Variant summary

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

The ENST00000554814.1(ENSG00000259035):​n.316-54056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,404 control chromosomes in the GnomAD database, including 7,324 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 0.30 (7324 hom., cov: 31)
• Consequence: ENSG00000259035 ENST00000554814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 3 publications found

Genes affected

ENSG00000259035 (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 (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984704	XR_007064292.1	n.842-97878G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259035	ENST00000554814.1	n.316-54056G>A		intron_variant	Intron 3 of 3	4
ENSG00000295274	ENST00000728943.1	n.264+1451G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45335 AN: 151288 Hom.: 7311 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.300 AC: 45377 AN: 151404 Hom.: 7324 Cov.: 31 AF XY: 0.303 AC XY: 22421 AN XY: 73906

African (AFR) AF: 0.172 AC: 7111 AN: 41332

American (AMR) AF: 0.339 AC: 5139 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1264 AN: 3458

East Asian (EAS) AF: 0.369 AC: 1883 AN: 5104

South Asian (SAS) AF: 0.374 AC: 1793 AN: 4790

European-Finnish (FIN) AF: 0.365 AC: 3840 AN: 10512

Middle Eastern (MID) AF: 0.372 AC: 108 AN: 290

European-Non Finnish (NFE) AF: 0.342 AC: 23188 AN: 67738

Other (OTH) AF: 0.341 AC: 716 AN: 2102

Alfa AF: 0.312 Hom.: 4247

Bravo AF: 0.291

Asia WGS AF: 0.377 AC: 1312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.60
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1210840; hg19: chr14-82442394;