chr10-44318290-T-C

Variant names:

• chr10-44318290-T-C
• rs2146807
• ENST00000732418.1:n.330A>G

Variant summary

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

The ENST00000732418.1(ENSG00000295748):​n.330A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,208 control chromosomes in the GnomAD database, including 2,147 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 0.16 (2147 hom., cov: 32)
• Consequence: ENSG00000295748 ENST00000732418.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 6 publications found

Genes affected

ENSG00000295748 (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 (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732418.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295748	ENST00000732418.1		n.330A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000295737	ENST00000732270.1		n.268+7391T>C		intron	N/A
	ENSG00000295737	ENST00000732271.1		n.203+7424T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24612 AN: 152090 Hom.: 2142 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.162 AC: 24642 AN: 152208 Hom.: 2147 Cov.: 32 AF XY: 0.163 AC XY: 12157 AN XY: 74434

African (AFR) AF: 0.215 AC: 8932 AN: 41500

American (AMR) AF: 0.202 AC: 3084 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 616 AN: 3472

East Asian (EAS) AF: 0.0996 AC: 516 AN: 5182

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4818

European-Finnish (FIN) AF: 0.0827 AC: 879 AN: 10624

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8991 AN: 68014

Other (OTH) AF: 0.161 AC: 339 AN: 2106

Alfa AF: 0.143 Hom.: 2091

Bravo AF: 0.172

Asia WGS AF: 0.169 AC: 593 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	6.2
DANN	Benign	0.63
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2146807;

hg19: chr10-44813738;