rs1121704

Positions:

• chr14-98085829-G-A

Variant summary

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

The ENST00000555776.1(ENSG00000259097):​n.122-5304C>T 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 0.342 in 151,976 control chromosomes in the GnomAD database, including 9,226 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 0.34 (9226 hom., cov: 32)
• Consequence: ENST00000555776.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370655	XR_001750876.2	n.96-5304C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555776.1	n.122-5304C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000663808.1	n.205-5304C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51990 AN: 151858 Hom.: 9226 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.342 AC: 52012 AN: 151976 Hom.: 9226 Cov.: 32 AF XY: 0.338 AC XY: 25093 AN XY: 74264

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.356

Alfa AF: 0.356 Hom.: 1185

Bravo AF: 0.335

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1121704; hg19: chr14-98552166;