rs10485351

Variant names:

• chr6-167783678-G-A
• rs10485351
• ENST00000794551.1:n.442-1772C>T

Variant summary

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

The ENST00000794551.1(AFDN-DT):​n.442-1772C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,200 control chromosomes in the GnomAD database, including 1,646 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 0.13 (1646 hom., cov: 33)
• Consequence: AFDN-DT ENST00000794551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 0 publications found

Genes affected

AFDN-DT (HGNC:21236): (AFDN divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AFDN-DT	ENST00000794551.1	n.442-1772C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19303 AN: 152082 Hom.: 1649 Cov.: 33

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.127 AC: 19296 AN: 152200 Hom.: 1646 Cov.: 33 AF XY: 0.123 AC XY: 9182 AN XY: 74412

African (AFR) AF: 0.0338 AC: 1402 AN: 41534

American (AMR) AF: 0.119 AC: 1822 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5184

South Asian (SAS) AF: 0.130 AC: 629 AN: 4826

European-Finnish (FIN) AF: 0.145 AC: 1536 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12611 AN: 67992

Other (OTH) AF: 0.144 AC: 304 AN: 2110

Alfa AF: 0.157 Hom.: 3622

Bravo AF: 0.123

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.83
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10485351; hg19: chr6-168184358;