chr10-44401541-G-A

Variant names:

• chr10-44401541-G-A
• rs1761325
• XR_001747298.2:n.2921G>A

Variant summary

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

The XR_001747298.2(LOC107984179):​n.2921G>A 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 0.161 in 151,852 control chromosomes in the GnomAD database, including 2,156 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 (2156 hom., cov: 33)
• Consequence: LOC107984179 XR_001747298.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 1 publications found

Genes affected

LOC107984179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791650.1. 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
	ENSG00000303087	ENST00000791650.1		n.488-168G>A		intron	N/A
	ENSG00000303074	ENST00000791579.1		n.-132G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24379 AN: 151734 Hom.: 2152 Cov.: 33

Gnomad AFR AF: 0.0747

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.161 AC: 24382 AN: 151852 Hom.: 2156 Cov.: 33 AF XY: 0.159 AC XY: 11789 AN XY: 74192

African (AFR) AF: 0.0744 AC: 3084 AN: 41428

American (AMR) AF: 0.140 AC: 2131 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1210 AN: 5158

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4808

European-Finnish (FIN) AF: 0.175 AC: 1838 AN: 10480

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.200 AC: 13566 AN: 67940

Other (OTH) AF: 0.159 AC: 335 AN: 2104

Alfa AF: 0.185 Hom.: 4752

Bravo AF: 0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.72
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs1761325; hg19: chr10-44896989; COSMIC: COSV55953557;