10-107692722-A-G

Variant names:

• chr10-107692722-A-G
• rs2245437
• ENST00000757237.1:n.67+3076A>G

Variant summary

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

The ENST00000757237.1(ENSG00000298678):​n.67+3076A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,060 control chromosomes in the GnomAD database, including 50,417 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 0.80 (50417 hom., cov: 31)
• Consequence: ENSG00000298678 ENST00000757237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

Genes affected

ENSG00000298678 (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 = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757237.1. 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
	ENSG00000298678	ENST00000757237.1		n.67+3076A>G		intron	N/A
	ENSG00000298678	ENST00000757238.1		n.54+3076A>G		intron	N/A
	ENSG00000298678	ENST00000757239.1		n.91+3076A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122085 AN: 151942 Hom.: 50402 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.803 AC: 122142 AN: 152060 Hom.: 50417 Cov.: 31 AF XY: 0.803 AC XY: 59677 AN XY: 74338

African (AFR) AF: 0.595 AC: 24625 AN: 41406

American (AMR) AF: 0.820 AC: 12527 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2977 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4599 AN: 5174

South Asian (SAS) AF: 0.735 AC: 3541 AN: 4818

European-Finnish (FIN) AF: 0.930 AC: 9857 AN: 10596

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61181 AN: 67998

Other (OTH) AF: 0.820 AC: 1726 AN: 2106

Alfa AF: 0.862 Hom.: 96813

Bravo AF: 0.789

Asia WGS AF: 0.793 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.44
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2245437; hg19: chr10-109452480;