chr10-5283724-G-A

Variant names:

• chr10-5283724-G-A
• rs9423590
• ENST00000305623.12:n.412C>T

Variant summary

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

The ENST00000432689.2(ENSG00000291045):​n.262C>T 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 0.141 in 159,322 control chromosomes in the GnomAD database, including 2,033 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 0.14 (1876 hom., cov: 32)
  • Exomes 𝑓: 0.20 (157 hom.)
• Consequence: ENSG00000291045 ENST00000432689.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 6 publications found

Genes affected

AKR1C7P (HGNC:44681): (aldo-keto reductase family 1 member C7, pseudogene)

ENSG00000291045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432689.2. 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
	AKR1C7P	ENST00000305623.12	TSL:6	n.412C>T		non_coding_transcript_exon	Exon 4 of 8
	ENSG00000291045	ENST00000432689.2	TSL:3	n.262C>T		non_coding_transcript_exon	Exon 3 of 6
	ENSG00000291045	ENST00000701390.2		n.355C>T		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20919 AN: 151972 Hom.: 1875 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.204 AC: 1477 AN: 7232 Hom.: 157 Cov.: 0 AF XY: 0.199 AC XY: 717 AN XY: 3594

African (AFR) AF: 0.0286 AC: 2 AN: 70

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.163 AC: 14 AN: 86

European-Finnish (FIN) AF: 0.234 AC: 1193 AN: 5090

Middle Eastern (MID) AF: 0.127 AC: 207 AN: 1624

European-Non Finnish (NFE) AF: 0.222 AC: 32 AN: 144

Other (OTH) AF: 0.129 AC: 27 AN: 210

GnomAD4 genome AF: 0.138 AC: 20918 AN: 152090 Hom.: 1876 Cov.: 32 AF XY: 0.135 AC XY: 10060 AN XY: 74344

African (AFR) AF: 0.0444 AC: 1842 AN: 41492

American (AMR) AF: 0.148 AC: 2271 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5174

South Asian (SAS) AF: 0.0849 AC: 409 AN: 4820

European-Finnish (FIN) AF: 0.182 AC: 1918 AN: 10556

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13501 AN: 67966

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.160 Hom.: 1253

Bravo AF: 0.132

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-2.0

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: rs9423590;

hg19: chr10-5325687;