chr5-144939990-A-T

Position:

• chr5-144939990-A-T

Variant summary

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

The ENST00000659832.1(ENSG00000251031):​n.182+26746T>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 0.306 in 150,314 control chromosomes in the GnomAD database, including 7,170 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 0.31 (7170 hom., cov: 31)
• Consequence: ENST00000659832.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000659832.1	n.182+26746T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.306 AC: 45928 AN: 150212 Hom.: 7169 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.306 AC: 45934 AN: 150314 Hom.: 7170 Cov.: 31 AF XY: 0.305 AC XY: 22363 AN XY: 73346

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.308

Alfa AF: 0.132 Hom.: 215

Bravo AF: 0.308

Asia WGS AF: 0.257 AC: 893 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2108661; hg19: chr5-144319553;