3-127242305-C-T

Variant names:

• chr3-127242305-C-T
• rs13075436
• ENST00000716127.1:n.112+14786C>T

Variant summary

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

The ENST00000716127.1(ENSG00000289641):​n.112+14786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,866 control chromosomes in the GnomAD database, including 9,003 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 (9003 hom., cov: 32)
• Consequence: ENSG00000289641 ENST00000716127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

Genes affected

ENSG00000289641 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 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
ENSG00000289641	ENST00000716127.1	n.112+14786C>T		intron_variant	Intron 1 of 2
ENSG00000289641	ENST00000826701.1	n.519+20445C>T		intron_variant	Intron 2 of 2
ENSG00000289641	ENST00000826702.1	n.126+14786C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50910 AN: 151748 Hom.: 9006 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.335 AC: 50926 AN: 151866 Hom.: 9003 Cov.: 32 AF XY: 0.332 AC XY: 24667 AN XY: 74210

African (AFR) AF: 0.233 AC: 9665 AN: 41394

American (AMR) AF: 0.303 AC: 4618 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.242 AC: 1245 AN: 5152

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3958 AN: 10502

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.400 AC: 27177 AN: 67960

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.369 Hom.: 18742

Bravo AF: 0.325

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13075436; hg19: chr3-126961148;