rs1800760

Positions:

• chr4-99144475-A-T

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.680-10070A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,080 control chromosomes in the GnomAD database, including 10,416 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 0.34 (10416 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.680-10070A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.680-10070A>T		intron_variant		1
ADH4	ENST00000504581.1	n.170-1695T>A		intron_variant		3
ENSG00000246090	ENST00000661393.1	n.676+10670A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51596 AN: 151962 Hom.: 10413 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.339 AC: 51602 AN: 152080 Hom.: 10416 Cov.: 32 AF XY: 0.342 AC XY: 25445 AN XY: 74334

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.355

Alfa AF: 0.392 Hom.: 1596

Bravo AF: 0.315

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.50
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800760; hg19: chr4-100065626;