rs12570371

Variant names:

• chr10-52787697-A-G
• rs12570371
• ENST00000816733.1:n.505-2501A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-52787697-A-G
• chr10-52787697-A-T

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.505-2501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,776 control chromosomes in the GnomAD database, including 38,265 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 0.71 (38265 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 3 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816733.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306279	ENST00000816733.1		n.505-2501A>G		intron	N/A
	ENSG00000306279	ENST00000816734.1		n.382-2501A>G		intron	N/A
	ENSG00000306279	ENST00000816735.1		n.98-2501A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106915 AN: 151658 Hom.: 38214 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.705 AC: 107028 AN: 151776 Hom.: 38265 Cov.: 32 AF XY: 0.708 AC XY: 52517 AN XY: 74170

African (AFR) AF: 0.597 AC: 24618 AN: 41204

American (AMR) AF: 0.784 AC: 11973 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4309 AN: 5170

South Asian (SAS) AF: 0.690 AC: 3315 AN: 4802

European-Finnish (FIN) AF: 0.750 AC: 7912 AN: 10554

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.731 AC: 49727 AN: 67982

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

Alfa AF: 0.720 Hom.: 20054

Bravo AF: 0.708

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.025
DANN	Benign	0.42
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12570371;

hg19: chr10-54547457;