rs1781930

Variant names:

• chr10-5154078-G-A
• rs1781930
• NM_001395972.1:c.*62C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-5154078-G-A
• chr10-5154078-G-C

Variant summary

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

The NM_001395972.1(AKR1C8):​c.*62C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 451,612 control chromosomes in the GnomAD database, including 5,360 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 0.13 (1513 hom., cov: 32)
  • Exomes 𝑓: 0.15 (3847 hom.)
• Consequence: AKR1C8 NM_001395972.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 8 publications found

Genes affected

AKR1C8 (HGNC:23469): (aldo-keto reductase family 1 member C8) Predicted to enable D-threo-aldose 1-dehydrogenase activity; aldo-keto reductase (NADP) activity; and estradiol 17-beta-dehydrogenase activity. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 (AMR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395972.1. 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
	AKR1C8	NM_001395972.1	MANE Select	c.*62C>T		3_prime_UTR	Exon 9 of 9	NP_001382901.1
	AKR1C8	NR_027916.3		n.2527C>T		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKR1C8	ENST00000648824.2	MANE Select	c.*62C>T		3_prime_UTR	Exon 9 of 9	ENSP00000496804.1
	AKR1C8	ENST00000584929.7	TSL:6	n.*709C>T		downstream_gene	N/A	ENSP00000496857.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19454 AN: 151956 Hom.: 1510 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.153 AC: 45924 AN: 299538 Hom.: 3847 AF XY: 0.150 AC XY: 25533 AN XY: 169814

African (AFR) AF: 0.0359 AC: 295 AN: 8214

American (AMR) AF: 0.196 AC: 5079 AN: 25978

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 1096 AN: 10076

East Asian (EAS) AF: 0.133 AC: 1211 AN: 9072

South Asian (SAS) AF: 0.121 AC: 6718 AN: 55462

European-Finnish (FIN) AF: 0.165 AC: 4273 AN: 25912

Middle Eastern (MID) AF: 0.0724 AC: 157 AN: 2168

European-Non Finnish (NFE) AF: 0.168 AC: 25147 AN: 149296

Other (OTH) AF: 0.146 AC: 1948 AN: 13360

GnomAD4 genome AF: 0.128 AC: 19457 AN: 152074 Hom.: 1513 Cov.: 32 AF XY: 0.130 AC XY: 9650 AN XY: 74342

African (AFR) AF: 0.0372 AC: 1543 AN: 41498

American (AMR) AF: 0.173 AC: 2637 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.137 AC: 707 AN: 5166

South Asian (SAS) AF: 0.129 AC: 623 AN: 4818

European-Finnish (FIN) AF: 0.171 AC: 1811 AN: 10564

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11444 AN: 67964

Other (OTH) AF: 0.107 AC: 225 AN: 2110

Alfa AF: 0.156 Hom.: 7707

Bravo AF: 0.124

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1781930; hg19: chr10-5196273;