10-79935194-G-A

Variant names:

• chr10-79935194-G-A
• rs1923539
• ENST00000421889.1:n.109-1337G>A

Variant summary

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

The ENST00000421889.1(ENSG00000283913):​n.109-1337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,008 control chromosomes in the GnomAD database, including 3,144 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 0.19 (3144 hom., cov: 31)
• Consequence: ENSG00000283913 ENST00000421889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 14 publications found

Genes affected

ENSG00000283913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421889.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000421889.1	TSL:3	n.109-1337G>A		intron	N/A
	ENSG00000283913	ENST00000453174.7	TSL:2	n.836-1337G>A		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.634-14834G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28131 AN: 151890 Hom.: 3145 Cov.: 31

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.185 AC: 28135 AN: 152008 Hom.: 3144 Cov.: 31 AF XY: 0.186 AC XY: 13820 AN XY: 74286

African (AFR) AF: 0.0698 AC: 2896 AN: 41466

American (AMR) AF: 0.134 AC: 2052 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 730 AN: 3460

East Asian (EAS) AF: 0.190 AC: 979 AN: 5160

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4818

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10542

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.248 AC: 16840 AN: 67968

Other (OTH) AF: 0.178 AC: 376 AN: 2116

Alfa AF: 0.223 Hom.: 8533

Bravo AF: 0.167

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.35
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1923539; hg19: chr10-81694950;