rs1198030

chr14-81977931-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554814.1(ENSG00000259035):n.316-52175G>A variant causes a intron, non coding transcript 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: ENST00000554814.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107984704	XR_007064292.1	n.842-95997G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554814.1	n.316-52175G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.340

Alfa AF: 0.330 Hom.: 4328

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1198030; hg19: chr14-82444275;