chr1-63322420-G-T

Position:

• chr1-63322420-G-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Moderate BS2

The ENST00000418244.6(FOXD3-AS1):​n.82C>A 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 0.00181 in 985,574 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency:
  • Genomes: 𝑓 0.0013 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0019 (4 hom.)
• Consequence: FOXD3-AS1 ENST00000418244.6 non_coding_transcript_exon
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -3.26

Genes affected

FOXD3-AS1 (HGNC:40241): (FOXD3 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BS2: High Homozygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FOXD3-AS1	NR_121637.1	n.88-957C>A		intron_variant, non_coding_transcript_variant
FOXD3-AS1	NR_121634.1	n.39C>A		non_coding_transcript_exon_variant	1/4
FOXD3-AS1	NR_121635.1	n.39C>A		non_coding_transcript_exon_variant	1/3
FOXD3-AS1	NR_121636.1	n.186-957C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FOXD3-AS1	ENST00000427268.1	n.88-957C>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00134 AC: 204 AN: 152256 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.00691

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00931

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.00190 AC: 1579 AN: 833200 Hom.: 4 Cov.: 29 AF XY: 0.00201 AC XY: 773 AN XY: 384788

Gnomad4 AFR exome AF: 0.000127

Gnomad4 AMR exome AF: 0.00203

Gnomad4 ASJ exome AF: 0.00272

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0113

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00163

Gnomad4 OTH exome AF: 0.00399

GnomAD4 genome AF: 0.00135 AC: 205 AN: 152374 Hom.: 0 Cov.: 33 AF XY: 0.00134 AC XY: 100 AN XY: 74506

Gnomad4 AFR AF: 0.000168

Gnomad4 AMR AF: 0.000522

Gnomad4 ASJ AF: 0.00691

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00952

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00169

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00137 Hom.: 0

Bravo AF: 0.00107

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Autoimmune disease, susceptibility to, 1 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Aug 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	1.7
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41285370; hg19: chr1-63788091;