10-7102293-T-G

Variant names:

• chr10-7102293-T-G
• rs2462692
• ENST00000664549.1:n.190+15987A>C

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.190+15987A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,264 control chromosomes in the GnomAD database, including 69,080 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 0.95 (69080 hom., cov: 31)
• Consequence: ENSG00000287277 ENST00000664549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 1 publications found

Genes affected

ENSG00000287277 (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 = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664549.1. 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
	LOC105376387	NR_188183.1		n.190+15987A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287277	ENST00000664549.1		n.190+15987A>C		intron	N/A
	ENSG00000287277	ENST00000666104.1		n.135+15987A>C		intron	N/A
	ENSG00000287277	ENST00000668409.1		n.153+15987A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144906 AN: 152146 Hom.: 69034 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.952 AC: 145011 AN: 152264 Hom.: 69080 Cov.: 31 AF XY: 0.954 AC XY: 71014 AN XY: 74446

African (AFR) AF: 0.970 AC: 40306 AN: 41552

American (AMR) AF: 0.953 AC: 14582 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3319 AN: 3468

East Asian (EAS) AF: 0.988 AC: 5104 AN: 5166

South Asian (SAS) AF: 0.979 AC: 4722 AN: 4822

European-Finnish (FIN) AF: 0.960 AC: 10182 AN: 10604

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.936 AC: 63646 AN: 68032

Other (OTH) AF: 0.951 AC: 2011 AN: 2114

Alfa AF: 0.930 Hom.: 25210

Bravo AF: 0.952

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs2462692; hg19: chr10-7144255;