22-23618000-C-T

Position:

• chr22-23618000-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016449.4(DRICH1):​c.437-343G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,858 control chromosomes in the GnomAD database, including 15,429 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 (15429 hom., cov: 32)
• Consequence: DRICH1 NM_016449.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.31

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DRICH1	NM_016449.4	c.437-343G>A		intron_variant		ENST00000317749.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRICH1	ENST00000317749.9	c.437-343G>A		intron_variant		1	NM_016449.4	P1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67836 AN: 151740 Hom.: 15408 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.447 AC: 67903 AN: 151858 Hom.: 15429 Cov.: 32 AF XY: 0.442 AC XY: 32827 AN XY: 74226

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.464

Alfa AF: 0.445 Hom.: 22550

Bravo AF: 0.465

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.031
DANN	Benign	0.083

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6003815; hg19: chr22-23960187;