rs1676235

Positions:

• chr14-76552223-G-A
• chr14-76552223-G-C
• chr14-76552223-G-T

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.310+49254C>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 0.156 in 152,160 control chromosomes in the GnomAD database, including 2,467 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 0.16 (2467 hom., cov: 32)
• Consequence: ENST00000554926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554926.1	n.310+49254C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23709 AN: 152042 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0802

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.156 AC: 23690 AN: 152160 Hom.: 2467 Cov.: 32 AF XY: 0.151 AC XY: 11231 AN XY: 74376

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0790

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.173

Alfa AF: 0.190 Hom.: 1678

Bravo AF: 0.150

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1676235; hg19: chr14-77018566;