10-7112902-G-T

Variant names:

• chr10-7112902-G-T
• rs10905106
• ENST00000664549.1:n.190+5378C>A

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.190+5378C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,092 control chromosomes in the GnomAD database, including 5,046 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 0.23 (5046 hom., cov: 31)
• Consequence: ENSG00000287277 ENST00000664549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 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+5378C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287277	ENST00000664549.1		n.190+5378C>A		intron	N/A
	ENSG00000287277	ENST00000666104.1		n.135+5378C>A		intron	N/A
	ENSG00000287277	ENST00000668409.1		n.153+5378C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35216 AN: 151974 Hom.: 5044 Cov.: 31

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.232 AC: 35216 AN: 152092 Hom.: 5046 Cov.: 31 AF XY: 0.226 AC XY: 16824 AN XY: 74346

African (AFR) AF: 0.0777 AC: 3226 AN: 41504

American (AMR) AF: 0.227 AC: 3467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1086 AN: 3464

East Asian (EAS) AF: 0.0941 AC: 486 AN: 5166

South Asian (SAS) AF: 0.163 AC: 786 AN: 4818

European-Finnish (FIN) AF: 0.249 AC: 2628 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22663 AN: 67968

Other (OTH) AF: 0.261 AC: 553 AN: 2116

Alfa AF: 0.301 Hom.: 16606

Bravo AF: 0.226

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.63
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10905106; hg19: chr10-7154864;