6-30870911-T-G

Position:

• chr6-30870911-T-G

Variant summary

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

The ENST00000458361.1(DDR1-DT):​n.1143-1078A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDR1-DT	ENST00000458361.1	n.1143-1078A>C		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.279

Alfa AF: 0.345 Hom.: 13211

Bravo AF: 0.263

Asia WGS AF: 0.212 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844654; hg19: chr6-30838688;