chr1-206893038-C-T

Variant names:

• chr1-206893038-C-T
• rs4845147
• ENST00000830172.1:n.177+2591G>A

Variant summary

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

The ENST00000830172.1(ENSG00000307982):​n.177+2591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,000 control chromosomes in the GnomAD database, including 16,983 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 0.47 (16983 hom., cov: 32)
• Consequence: ENSG00000307982 ENST00000830172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 6 publications found

Genes affected

ENSG00000307982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830172.1. 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
	ENSG00000307982	ENST00000830172.1		n.177+2591G>A		intron	N/A
	ENSG00000307982	ENST00000830173.1		n.69-1353G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70708 AN: 151882 Hom.: 16967 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70779 AN: 152000 Hom.: 16983 Cov.: 32 AF XY: 0.457 AC XY: 33951 AN XY: 74288

African (AFR) AF: 0.561 AC: 23260 AN: 41440

American (AMR) AF: 0.462 AC: 7050 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1145 AN: 5160

South Asian (SAS) AF: 0.234 AC: 1127 AN: 4810

European-Finnish (FIN) AF: 0.376 AC: 3969 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31001 AN: 67964

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.477 Hom.: 2458

Bravo AF: 0.477

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.34
DANN	Benign	0.65
PhyloP100		-0.20

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: rs4845147;

hg19: chr1-207066383;