rs1020344

Variant names:

• chr8-96445305-G-A
• rs1020344
• ENST00000787940.1:n.220-11984G>A

Variant summary

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

The ENST00000787940.1(ENSG00000302579):​n.220-11984G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,126 control chromosomes in the GnomAD database, including 7,536 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 0.23 (7536 hom., cov: 33)
• Consequence: ENSG00000302579 ENST00000787940.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 3 publications found

Genes affected

ENSG00000302579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375653	XR_928432.2	n.370-11984G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302579	ENST00000787940.1	n.220-11984G>A		intron_variant	Intron 2 of 3
ENSG00000302579	ENST00000787941.1	n.409-11984G>A		intron_variant	Intron 3 of 4
ENSG00000302579	ENST00000787942.1	n.318-11984G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35396 AN: 152008 Hom.: 7503 Cov.: 33

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.233 AC: 35479 AN: 152126 Hom.: 7536 Cov.: 33 AF XY: 0.233 AC XY: 17345 AN XY: 74374

African (AFR) AF: 0.570 AC: 23620 AN: 41450

American (AMR) AF: 0.116 AC: 1773 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.138 AC: 714 AN: 5174

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1490 AN: 10590

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.0882 AC: 6000 AN: 68012

Other (OTH) AF: 0.194 AC: 409 AN: 2112

Alfa AF: 0.125 Hom.: 3889

Bravo AF: 0.243

Asia WGS AF: 0.199 AC: 691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.74
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs1020344; hg19: chr8-97457533;