chr1-164261826-T-C

Variant names:

• chr1-164261826-T-C
• rs1338993
• ENST00000821208.1:n.159-1135T>C

Variant summary

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

The ENST00000821208.1(ENSG00000306805):​n.159-1135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,022 control chromosomes in the GnomAD database, including 13,181 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 0.40 (13181 hom., cov: 32)
• Consequence: ENSG00000306805 ENST00000821208.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 3 publications found

Genes affected

ENSG00000306805 (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 (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821208.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306805	ENST00000821208.1		n.159-1135T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61013 AN: 151906 Hom.: 13159 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.402 AC: 61092 AN: 152022 Hom.: 13181 Cov.: 32 AF XY: 0.401 AC XY: 29755 AN XY: 74272

African (AFR) AF: 0.535 AC: 22176 AN: 41464

American (AMR) AF: 0.393 AC: 5991 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3549 AN: 5148

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4820

European-Finnish (FIN) AF: 0.286 AC: 3027 AN: 10580

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22247 AN: 67964

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.370 Hom.: 3670

Bravo AF: 0.417

Asia WGS AF: 0.492 AC: 1709 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.70
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1338993; hg19: chr1-164231063;