rs13245201

Variant names:

• chr7-128237691-G-A
• rs13245201
• ENST00000785131.1:n.169-16151C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-128237691-G-A
• chr7-128237691-G-T

Variant summary

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

The ENST00000785131.1(ENSG00000289434):​n.169-16151C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,100 control chromosomes in the GnomAD database, including 12,816 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 0.37 (12816 hom., cov: 33)
• Consequence: ENSG00000289434 ENST00000785131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 6 publications found

Genes affected

ENSG00000289434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000289434	ENST00000785131.1	n.169-16151C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56843 AN: 151982 Hom.: 12812 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.374 AC: 56866 AN: 152100 Hom.: 12816 Cov.: 33 AF XY: 0.384 AC XY: 28573 AN XY: 74330

African (AFR) AF: 0.124 AC: 5149 AN: 41510

American (AMR) AF: 0.436 AC: 6657 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3466

East Asian (EAS) AF: 0.745 AC: 3857 AN: 5180

South Asian (SAS) AF: 0.525 AC: 2528 AN: 4816

European-Finnish (FIN) AF: 0.509 AC: 5368 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30526 AN: 67988

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.409 Hom.: 20158

Bravo AF: 0.354

Asia WGS AF: 0.622 AC: 2160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.41
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs13245201; hg19: chr7-127877744;