14-81977931-G-A

Variant names:

• chr14-81977931-G-A
• rs1198030
• ENST00000554814.1:n.316-52175G>A

Variant summary

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

The ENST00000554814.1(ENSG00000259035):​n.316-52175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,974 control chromosomes in the GnomAD database, including 7,345 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 (7345 hom., cov: 32)
• Consequence: ENSG00000259035 ENST00000554814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984704	XR_007064292.1	n.842-95997G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259035	ENST00000554814.1	n.316-52175G>A		intron_variant	Intron 3 of 3	4
ENSG00000295274	ENST00000728943.1	n.264+3332G>A		intron_variant	Intron 1 of 1
ENSG00000289442	ENST00000729098.1	n.95-556C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45465 AN: 151856 Hom.: 7332 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.299 AC: 45507 AN: 151974 Hom.: 7345 Cov.: 32 AF XY: 0.303 AC XY: 22509 AN XY: 74274

African (AFR) AF: 0.172 AC: 7129 AN: 41496

American (AMR) AF: 0.338 AC: 5152 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3464

East Asian (EAS) AF: 0.369 AC: 1898 AN: 5144

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3846 AN: 10562

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23251 AN: 67940

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.329 Hom.: 4794

Bravo AF: 0.291

Asia WGS AF: 0.378 AC: 1313 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.68
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1198030; hg19: chr14-82444275;