rs6671200

Positions:

• chr1-95231973-A-C
• chr1-95231973-A-T

Variant summary

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

The NM_001199691.1(TLCD4-RWDD3):​c.566+979A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,320 control chromosomes in the GnomAD database, including 61,955 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 0.90 (61955 hom., cov: 35)
• Consequence: TLCD4-RWDD3 NM_001199691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791

Genes affected

TLCD4-RWDD3 (HGNC:):

RWDD3-DT (HGNC:55839): (RWDD3 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TLCD4-RWDD3	NM_001199691.1	c.566+979A>C		intron_variant			NP_001186620.1
RWDD3-DT	NR_125949.1	n.283+1727T>G		intron_variant, non_coding_transcript_variant
RWDD3-DT	NR_125948.1	n.283+1727T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RWDD3-DT	ENST00000663020.1	n.258+1727T>G		intron_variant, non_coding_transcript_variant
RWDD3-DT	ENST00000419846.1	n.280+1727T>G		intron_variant, non_coding_transcript_variant		3
RWDD3-DT	ENST00000421762.5	n.283+1727T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137092 AN: 152202 Hom.: 61911 Cov.: 35

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.901 AC: 137196 AN: 152320 Hom.: 61955 Cov.: 35 AF XY: 0.903 AC XY: 67269 AN XY: 74488

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.915

Alfa AF: 0.912 Hom.: 73797

Bravo AF: 0.899

Asia WGS AF: 0.982 AC: 3417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.1
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs6671200; hg19: chr1-95697529;