rs1414896

chr1-95226754-G-A

Variant summary

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

The NM_001199691.1(TLCD4-RWDD3):c.474-4148G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,000 control chromosomes in the GnomAD database, including 20,951 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 0.51 (20951 hom., cov: 32)
• Consequence: TLCD4-RWDD3 NM_001199691.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TLCD4-RWDD3	NM_001199691.1	c.474-4148G>A		intron_variant
RWDD3-DT	NR_125949.1	n.284-4923C>T		intron_variant, non_coding_transcript_variant
RWDD3-DT	NR_125948.1	n.284-4923C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RWDD3-DT	ENST00000663020.1	n.259-4923C>T		intron_variant, non_coding_transcript_variant
RWDD3-DT	ENST00000419846.1	n.281-4923C>T		intron_variant, non_coding_transcript_variant		3
RWDD3-DT	ENST00000421762.5	n.284-4923C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77282 AN: 151880 Hom.: 20951 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.509 AC: 77298 AN: 152000 Hom.: 20951 Cov.: 32 AF XY: 0.507 AC XY: 37669 AN XY: 74296

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.544

Alfa AF: 0.599 Hom.: 62004

Bravo AF: 0.497

Asia WGS AF: 0.492 AC: 1715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.75

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: rs1414896; hg19: chr1-95692310;