10-10254156-G-T

Variant names:

• chr10-10254156-G-T
• rs7097577
• ENST00000738164.1:n.300-32678G>T

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.300-32678G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.953 in 152,268 control chromosomes in the GnomAD database, including 69,561 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 (69561 hom., cov: 32)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 3 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738164.1. 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
	ENSG00000296323	ENST00000738164.1		n.300-32678G>T		intron	N/A
	ENSG00000296323	ENST00000738165.1		n.327-32678G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145087 AN: 152150 Hom.: 69528 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.985

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.953 AC: 145177 AN: 152268 Hom.: 69561 Cov.: 32 AF XY: 0.955 AC XY: 71097 AN XY: 74450

African (AFR) AF: 0.850 AC: 35279 AN: 41518

American (AMR) AF: 0.975 AC: 14909 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3469 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5178

South Asian (SAS) AF: 0.985 AC: 4752 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10621 AN: 10624

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67776 AN: 68040

Other (OTH) AF: 0.967 AC: 2043 AN: 2112

Alfa AF: 0.971 Hom.: 114631

Bravo AF: 0.946

Asia WGS AF: 0.988 AC: 3433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.34
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7097577; hg19: chr10-10296119;