1-221100362-G-T

Variant names:

• chr1-221100362-G-T
• rs6541172
• ENST00000739959.1:n.95-4671G>T

Variant summary

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

The ENST00000739959.1(ENSG00000296502):​n.95-4671G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,196 control chromosomes in the GnomAD database, including 59,989 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 0.89 (59989 hom., cov: 31)
• Consequence: ENSG00000296502 ENST00000739959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 3 publications found

Genes affected

ENSG00000296502 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000739959.1. 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
	ENSG00000296502	ENST00000739959.1		n.95-4671G>T		intron	N/A
	ENSG00000296502	ENST00000739960.1		n.94+4201G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134799 AN: 152078 Hom.: 59934 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.886 AC: 134910 AN: 152196 Hom.: 59989 Cov.: 31 AF XY: 0.883 AC XY: 65668 AN XY: 74396

African (AFR) AF: 0.937 AC: 38884 AN: 41520

American (AMR) AF: 0.774 AC: 11830 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3179 AN: 3472

East Asian (EAS) AF: 0.817 AC: 4218 AN: 5164

South Asian (SAS) AF: 0.890 AC: 4297 AN: 4826

European-Finnish (FIN) AF: 0.874 AC: 9259 AN: 10592

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60343 AN: 68016

Other (OTH) AF: 0.873 AC: 1848 AN: 2116

Alfa AF: 0.871 Hom.: 9834

Bravo AF: 0.876

Asia WGS AF: 0.844 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6541172;

hg19: chr1-221273704;