rs1001161

Variant names:

• chr14-53589909-G-A
• rs1001161
• ENST00000456100.6:n.326-97290G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-53589909-G-A
• chr14-53589909-G-C
• chr14-53589909-G-T

Variant summary

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

The ENST00000456100.6(DDHD1-DT):​n.326-97290G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,180 control chromosomes in the GnomAD database, including 1,920 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 0.15 (1920 hom., cov: 32)
• Consequence: DDHD1-DT ENST00000456100.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 5 publications found

Genes affected

DDHD1-DT (HGNC:55441): (DDHD1 divergent transcript)

ENSG00000225680 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456100.6. 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
	DDHD1-DT	ENST00000456100.6	TSL:4	n.326-97290G>A		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-97290G>A		intron	N/A
	DDHD1-DT	ENST00000655713.1		n.439-1226G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22315 AN: 152062 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.0769

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.147 AC: 22307 AN: 152180 Hom.: 1920 Cov.: 32 AF XY: 0.143 AC XY: 10665 AN XY: 74402

African (AFR) AF: 0.0767 AC: 3186 AN: 41548

American (AMR) AF: 0.132 AC: 2016 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3472

East Asian (EAS) AF: 0.0357 AC: 185 AN: 5178

South Asian (SAS) AF: 0.0883 AC: 426 AN: 4826

European-Finnish (FIN) AF: 0.150 AC: 1591 AN: 10582

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13606 AN: 67986

Other (OTH) AF: 0.174 AC: 367 AN: 2110

Alfa AF: 0.183 Hom.: 4709

Bravo AF: 0.140

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.1
DANN	Benign	0.65
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1001161; hg19: chr14-54056627;