rs6713510

Variant names:

• chr2-226169783-G-A
• rs6713510
• ENST00000719962.1:n.93+15537C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-226169783-G-A
• chr2-226169783-G-C
• chr2-226169783-G-T

Variant summary

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

The ENST00000719962.1(ENSG00000235070):​n.93+15537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,914 control chromosomes in the GnomAD database, including 23,684 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 0.55 (23684 hom., cov: 31)
• Consequence: ENSG00000235070 ENST00000719962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 13 publications found

Genes affected

ENSG00000235070 (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 (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646736	NR_046102.1	n.504+4560G>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235070	ENST00000719962.1	n.93+15537C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83480 AN: 151798 Hom.: 23646 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.550 AC: 83560 AN: 151914 Hom.: 23684 Cov.: 31 AF XY: 0.555 AC XY: 41200 AN XY: 74256

African (AFR) AF: 0.688 AC: 28515 AN: 41428

American (AMR) AF: 0.549 AC: 8379 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3468

East Asian (EAS) AF: 0.598 AC: 3086 AN: 5160

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4818

European-Finnish (FIN) AF: 0.591 AC: 6240 AN: 10552

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32118 AN: 67914

Other (OTH) AF: 0.514 AC: 1088 AN: 2116

Alfa AF: 0.495 Hom.: 24737

Bravo AF: 0.557

Asia WGS AF: 0.443 AC: 1540 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	0.27
DANN	Benign	0.66
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6713510; hg19: chr2-227034499;