rs72626594

Variant names:

• chr20-56960465-G-A
• rs72626594
• ENST00000794105.1:n.88-2175G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000794105.1(ENSG00000303393):​n.88-2175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00328 in 152,260 control chromosomes in the GnomAD database, including 9 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 0.0033 (9 hom., cov: 33)
• Consequence: ENSG00000303393 ENST00000794105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.847
• Publications: 2 publications found

Genes affected

ENSG00000303393 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00328 (499/152260) while in subpopulation EAS AF = 0.048 (248/5166). AF 95% confidence interval is 0.0431. There are 9 homozygotes in GnomAd4. There are 303 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 gene

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
ENSG00000303393	ENST00000794105.1	n.88-2175G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00326 AC: 496 AN: 152142 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00923

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.00456

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.00334

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

GnomAD4 genome AF: 0.00328 AC: 499 AN: 152260 Hom.: 9 Cov.: 33 AF XY: 0.00407 AC XY: 303 AN XY: 74456

African (AFR) AF: 0.0000962 AC: 4 AN: 41564

American (AMR) AF: 0.00941 AC: 144 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00490 AC: 17 AN: 3468

East Asian (EAS) AF: 0.0480 AC: 248 AN: 5166

South Asian (SAS) AF: 0.00456 AC: 22 AN: 4824

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 68008

Other (OTH) AF: 0.00331 AC: 7 AN: 2116

Alfa AF: 0.00175 Hom.: 0

Bravo AF: 0.00430

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.6
DANN	Benign	0.85
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs72626594; hg19: chr20-55535521;