rs1198030

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554814.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259035	ENST00000554814.1	TSL:4	n.316-52175G>A		intron	N/A
	ENSG00000295274	ENST00000728943.1		n.264+3332G>A		intron	N/A
	ENSG00000289442	ENST00000729098.1		n.95-556C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1198030;

hg19: chr14-82444275;