chr6-30870911-T-G

Variant names:

• chr6-30870911-T-G
• rs2844654
• ENST00000458361.1:n.1143-1078A>C

Variant summary

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

The ENST00000458361.1(DDR1-DT):​n.1143-1078A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,112 control chromosomes in the GnomAD database, including 6,848 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 0.28 (6848 hom., cov: 30)
• Consequence: DDR1-DT ENST00000458361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 31 publications found

Genes affected

DDR1-DT (HGNC:28694): (DDR1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000458361.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDR1-DT	ENST00000458361.1	TSL:1	n.1143-1078A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42580 AN: 151994 Hom.: 6850 Cov.: 30

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.280 AC: 42589 AN: 152112 Hom.: 6848 Cov.: 30 AF XY: 0.281 AC XY: 20900 AN XY: 74328

African (AFR) AF: 0.125 AC: 5174 AN: 41534

American (AMR) AF: 0.245 AC: 3745 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3466

East Asian (EAS) AF: 0.256 AC: 1320 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4828

European-Finnish (FIN) AF: 0.393 AC: 4146 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24609 AN: 67968

Other (OTH) AF: 0.279 AC: 589 AN: 2114

Alfa AF: 0.332 Hom.: 33745

Bravo AF: 0.263

Asia WGS AF: 0.212 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.34
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2844654; hg19: chr6-30838688;