3-39258666-T-C

Variant names:

• chr3-39258666-T-C
• rs17038640
• ENST00000656239.1:n.315T>C

Variant summary

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

The ENST00000656239.1(ENSG00000287958):​n.315T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,154 control chromosomes in the GnomAD database, including 7,731 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 0.29 (7731 hom., cov: 32)
• Consequence: ENSG00000287958 ENST00000656239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 10 publications found

Genes affected

ENSG00000287958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724104	XR_940742.4	n.469T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287958	ENST00000656239.1	n.315T>C		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000287958	ENST00000702477.2	n.469T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287958	ENST00000785475.1	n.161T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43467 AN: 152036 Hom.: 7731 Cov.: 32

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.286 AC: 43465 AN: 152154 Hom.: 7731 Cov.: 32 AF XY: 0.295 AC XY: 21934 AN XY: 74390

African (AFR) AF: 0.0843 AC: 3501 AN: 41520

American (AMR) AF: 0.422 AC: 6461 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1237 AN: 3464

East Asian (EAS) AF: 0.590 AC: 3052 AN: 5170

South Asian (SAS) AF: 0.442 AC: 2134 AN: 4824

European-Finnish (FIN) AF: 0.392 AC: 4152 AN: 10588

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21963 AN: 67984

Other (OTH) AF: 0.303 AC: 637 AN: 2104

Alfa AF: 0.314 Hom.: 10389

Bravo AF: 0.276

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs17038640; hg19: chr3-39300157;