10-110554249-T-C

Variant names:

• chr10-110554249-T-C
• rs7918064
• ENST00000728672.1:n.182-7962A>G

Variant summary

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

The ENST00000728672.1(ENSG00000295217):​n.182-7962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,086 control chromosomes in the GnomAD database, including 38,951 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 0.72 (38951 hom., cov: 32)
• Consequence: ENSG00000295217 ENST00000728672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 4 publications found

Genes affected

ENSG00000295217 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295217	ENST00000728672.1	n.182-7962A>G		intron_variant	Intron 1 of 2
ENSG00000295217	ENST00000728673.1	n.144-7962A>G		intron_variant	Intron 1 of 1
ENSG00000295217	ENST00000728674.1	n.196-6669A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108782 AN: 151968 Hom.: 38952 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.715 AC: 108811 AN: 152086 Hom.: 38951 Cov.: 32 AF XY: 0.714 AC XY: 53074 AN XY: 74326

African (AFR) AF: 0.699 AC: 28977 AN: 41476

American (AMR) AF: 0.714 AC: 10910 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3037 AN: 5172

South Asian (SAS) AF: 0.672 AC: 3234 AN: 4816

European-Finnish (FIN) AF: 0.742 AC: 7841 AN: 10566

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49910 AN: 67986

Other (OTH) AF: 0.698 AC: 1472 AN: 2110

Alfa AF: 0.725 Hom.: 114273

Bravo AF: 0.715

Asia WGS AF: 0.615 AC: 2142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs7918064; hg19: chr10-112314007;