chr2-941001-C-T

Variant names:

• chr2-941001-C-T
• rs4971342
• ENST00000758261.1:n.184-365C>T

Variant summary

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

The ENST00000758261.1(ENSG00000298835):​n.184-365C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,156 control chromosomes in the GnomAD database, including 2,661 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 0.17 (2661 hom., cov: 32)
• Consequence: ENSG00000298835 ENST00000758261.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 4 publications found

Genes affected

ENSG00000298835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758261.1. 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
	ENSG00000298835	ENST00000758261.1		n.184-365C>T		intron	N/A
	ENSG00000298835	ENST00000758262.1		n.148-365C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26026 AN: 152038 Hom.: 2660 Cov.: 32

Gnomad AFR AF: 0.0927

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.171 AC: 26038 AN: 152156 Hom.: 2661 Cov.: 32 AF XY: 0.168 AC XY: 12497 AN XY: 74394

African (AFR) AF: 0.0928 AC: 3854 AN: 41516

American (AMR) AF: 0.139 AC: 2123 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3472

East Asian (EAS) AF: 0.0300 AC: 155 AN: 5174

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4820

European-Finnish (FIN) AF: 0.232 AC: 2454 AN: 10588

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15929 AN: 67974

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.203 Hom.: 6672

Bravo AF: 0.160

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4971342; hg19: chr2-936687;