rs210327

Variant names:

• chr14-53602063-C-A
• rs210327
• XR_007064176.1:n.9020G>T

Variant summary

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

The XR_007064176.1(LOC124903316):​n.9020G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,050 control chromosomes in the GnomAD database, including 30,045 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 0.62 (30045 hom., cov: 32)
• Consequence: LOC124903316 XR_007064176.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 6 publications found

Genes affected

LOC124903316 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436530.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225680	ENST00000436530.1	TSL:3	n.375-1880G>T		intron	N/A
	DDHD1-DT	ENST00000456100.6	TSL:4	n.326-85136C>A		intron	N/A
	DDHD1-DT	ENST00000648066.2		n.675-85136C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93873 AN: 151932 Hom.: 29989 Cov.: 32

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.618 AC: 93991 AN: 152050 Hom.: 30045 Cov.: 32 AF XY: 0.610 AC XY: 45361 AN XY: 74310

African (AFR) AF: 0.793 AC: 32889 AN: 41476

American (AMR) AF: 0.531 AC: 8103 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2181 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1709 AN: 5168

South Asian (SAS) AF: 0.628 AC: 3029 AN: 4820

European-Finnish (FIN) AF: 0.526 AC: 5555 AN: 10560

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.567 AC: 38535 AN: 67972

Other (OTH) AF: 0.614 AC: 1299 AN: 2114

Alfa AF: 0.582 Hom.: 55591

Bravo AF: 0.621

Asia WGS AF: 0.512 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.26
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs210327; hg19: chr14-54068781;