ENST00000771979.1:n.145+2438C>T

Variant names:

• chr17-70294992-C-T
• rs6501384
• ENST00000771979.1:n.145+2438C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000771979.1(ENSG00000300458):​n.145+2438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 151,932 control chromosomes in the GnomAD database, including 9,045 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 (9045 hom., cov: 32)
• Consequence: ENSG00000300458 ENST00000771979.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 18 publications found

Genes affected

ENSG00000300458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300458	ENST00000771979.1	n.145+2438C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51989 AN: 151814 Hom.: 9037 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.342 AC: 52030 AN: 151932 Hom.: 9045 Cov.: 32 AF XY: 0.340 AC XY: 25240 AN XY: 74262

African (AFR) AF: 0.372 AC: 15400 AN: 41430

American (AMR) AF: 0.300 AC: 4575 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3468

East Asian (EAS) AF: 0.172 AC: 887 AN: 5168

South Asian (SAS) AF: 0.440 AC: 2115 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 2998 AN: 10542

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23657 AN: 67932

Other (OTH) AF: 0.356 AC: 750 AN: 2108

Alfa AF: 0.344 Hom.: 41932

Bravo AF: 0.339

Asia WGS AF: 0.337 AC: 1170 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	0.42
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs6501384; hg19: chr17-68291133;