rs578935

Variant names:

• chr2-136453421-T-C
• rs578935
• ENST00000814599.1:n.99-1517T>C

Variant summary

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

The ENST00000814599.1(ENSG00000305987):​n.99-1517T>C 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 152,210 control chromosomes in the GnomAD database, including 1,403 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 (1403 hom., cov: 32)
• Consequence: ENSG00000305987 ENST00000814599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.00
• Publications: 3 publications found

Genes affected

ENSG00000305987 (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 = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814599.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305987	ENST00000814599.1		n.99-1517T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19306 AN: 152092 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.0932

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.127 AC: 19332 AN: 152210 Hom.: 1403 Cov.: 32 AF XY: 0.130 AC XY: 9635 AN XY: 74396

African (AFR) AF: 0.0935 AC: 3883 AN: 41546

American (AMR) AF: 0.142 AC: 2169 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1066 AN: 3464

East Asian (EAS) AF: 0.216 AC: 1119 AN: 5178

South Asian (SAS) AF: 0.227 AC: 1094 AN: 4814

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10608

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8256 AN: 68000

Other (OTH) AF: 0.174 AC: 367 AN: 2114

Alfa AF: 0.131 Hom.: 4793

Bravo AF: 0.124

Asia WGS AF: 0.236 AC: 823 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	7.9
DANN	Benign	0.72
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs578935; hg19: chr2-137210991;