1-72908338-C-T

Variant names:

• chr1-72908338-C-T
• rs2841181
• ENST00000758621.1:n.99-8765C>T

Variant summary

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

The ENST00000758621.1(ENSG00000298890):​n.99-8765C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,152 control chromosomes in the GnomAD database, including 67,233 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 0.94 (67233 hom., cov: 32)
• Consequence: ENSG00000298890 ENST00000758621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 0 publications found

Genes affected

ENSG00000298890 (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 = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758621.1. 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
	ENSG00000298890	ENST00000758621.1		n.99-8765C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.940 AC: 142890 AN: 152034 Hom.: 67191 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.940 AC: 142991 AN: 152152 Hom.: 67233 Cov.: 32 AF XY: 0.942 AC XY: 70091 AN XY: 74392

African (AFR) AF: 0.899 AC: 37315 AN: 41526

American (AMR) AF: 0.937 AC: 14289 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3391 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4597 AN: 5168

South Asian (SAS) AF: 0.952 AC: 4595 AN: 4826

European-Finnish (FIN) AF: 0.991 AC: 10519 AN: 10618

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65145 AN: 67978

Other (OTH) AF: 0.933 AC: 1969 AN: 2110

Alfa AF: 0.946 Hom.: 9333

Bravo AF: 0.933

Asia WGS AF: 0.903 AC: 3140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2841181; hg19: chr1-73374021;