rs10751776

Variant names:

• chr1-24970252-A-C
• rs10751776
• ENST00000568143.1:n.614T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-24970252-A-C
• chr1-24970252-A-T

Variant summary

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

The ENST00000568143.1(ENSG00000261025):​n.614T>G 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 0.619 in 152,152 control chromosomes in the GnomAD database, including 30,284 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 0.62 (30245 hom., cov: 31)
  • Exomes 𝑓: 0.61 (39 hom.)
• Consequence: ENSG00000261025 ENST00000568143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 13 publications found

Genes affected

ENSG00000261025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568143.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261025	ENST00000568143.1	TSL:6	n.614T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000261025	ENST00000751467.1		n.330+1025T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93880 AN: 151832 Hom.: 30191 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.614 AC: 124 AN: 202 Hom.: 39 Cov.: 0 AF XY: 0.615 AC XY: 91 AN XY: 148

African (AFR) AF: 0.833 AC: 5 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.633 AC: 19 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.597 AC: 86 AN: 144

Other (OTH) AF: 0.722 AC: 13 AN: 18

GnomAD4 genome AF: 0.619 AC: 93994 AN: 151950 Hom.: 30245 Cov.: 31 AF XY: 0.628 AC XY: 46635 AN XY: 74264

African (AFR) AF: 0.784 AC: 32507 AN: 41470

American (AMR) AF: 0.692 AC: 10571 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3646 AN: 5156

South Asian (SAS) AF: 0.672 AC: 3227 AN: 4804

European-Finnish (FIN) AF: 0.576 AC: 6079 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34107 AN: 67888

Other (OTH) AF: 0.610 AC: 1289 AN: 2112

Alfa AF: 0.648 Hom.: 12561

Bravo AF: 0.636

Asia WGS AF: 0.720 AC: 2505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.82
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10751776; hg19: chr1-25296743;