rs6003815

Variant names:

• chr22-23618000-C-T
• rs6003815
• NM_016449.4:c.437-343G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016449.4. 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
	DRICH1	NM_016449.4	MANE Select	c.437-343G>A		intron	N/A	NP_057533.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DRICH1	ENST00000317749.9	TSL:1 MANE Select	c.437-343G>A		intron	N/A	ENSP00000316137.5

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

African (AFR) AF: 0.466 AC: 19284 AN: 41370

American (AMR) AF: 0.564 AC: 8607 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1333 AN: 5174

South Asian (SAS) AF: 0.357 AC: 1719 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3923 AN: 10520

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30085 AN: 67938

Other (OTH) AF: 0.464 AC: 979 AN: 2108

Alfa AF: 0.446 Hom.: 33361

Bravo AF: 0.465

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.031
DANN	Benign	0.083
PhyloP100		-5.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6003815; hg19: chr22-23960187;