rs140174

Variant names:

• chr22-23580796-A-G
• rs140174
• ENST00000608615.1:n.*84T>C

Variant summary

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

The ENST00000608615.1(ENSG00000272733):​n.*84T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 153,562 control chromosomes in the GnomAD database, including 19,445 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 0.45 (19349 hom., cov: 32)
  • Exomes 𝑓: 0.35 (96 hom.)
• Consequence: ENSG00000272733 ENST00000608615.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 18 publications found

Genes affected

ENSG00000272733 (HGNC:):

DRICH1 (HGNC:28031): (aspartate rich 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRICH1	XM_011530206.2	c.*806T>C		downstream_gene_variant			XP_011528508.1
DRICH1	XM_047441388.1	c.*2375T>C		downstream_gene_variant			XP_047297344.1
DRICH1	XM_011530208.3	c.*2375T>C		downstream_gene_variant			XP_011528510.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272733	ENST00000608615.1	n.*84T>C		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68365 AN: 151962 Hom.: 19297 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.349 AC: 516 AN: 1480 Hom.: 96 AF XY: 0.344 AC XY: 269 AN XY: 782

African (AFR) AF: 0.688 AC: 11 AN: 16

American (AMR) AF: 0.473 AC: 191 AN: 404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.808 AC: 21 AN: 26

South Asian (SAS) AF: 0.526 AC: 40 AN: 76

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.258 AC: 231 AN: 896

Other (OTH) AF: 0.352 AC: 19 AN: 54

GnomAD4 genome AF: 0.450 AC: 68478 AN: 152082 Hom.: 19349 Cov.: 32 AF XY: 0.451 AC XY: 33562 AN XY: 74342

African (AFR) AF: 0.762 AC: 31614 AN: 41484

American (AMR) AF: 0.433 AC: 6609 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4101 AN: 5156

South Asian (SAS) AF: 0.473 AC: 2273 AN: 4808

European-Finnish (FIN) AF: 0.219 AC: 2323 AN: 10602

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18818 AN: 67970

Other (OTH) AF: 0.443 AC: 934 AN: 2110

Alfa AF: 0.342 Hom.: 40850

Bravo AF: 0.482

Asia WGS AF: 0.660 AC: 2291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		-0.73
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs140174; hg19: chr22-23922983;