rs2146807

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902544	XR_007062369.1	n.3743-20393A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295748	ENST00000732418.1	n.330A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000295737	ENST00000732270.1	n.268+7391T>C		intron_variant	Intron 1 of 2
ENSG00000295737	ENST00000732271.1	n.203+7424T>C		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2146807; hg19: chr10-44813738;