chr1-56386595-T-C

Variant names:

• chr1-56386595-T-C
• rs4431886
• ENST00000642129.1:n.*95+96668A>G

Variant summary

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

The ENST00000642129.1(ENSG00000284686):​n.*95+96668A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,198 control chromosomes in the GnomAD database, including 4,112 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 0.19 (4112 hom., cov: 32)
• Consequence: ENSG00000284686 ENST00000642129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.753
• Publications: 3 publications found

Genes affected

ENSG00000284686 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642129.1. 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
	ENSG00000284686	ENST00000642129.1		n.*95+96668A>G		intron	N/A	ENSP00000492927.1
	ENSG00000260971	ENST00000641035.1		n.555+90538A>G		intron	N/A
	ENSG00000284686	ENST00000641109.1		n.*321+92291A>G		intron	N/A	ENSP00000493138.1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28632 AN: 152080 Hom.: 4105 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.188 AC: 28683 AN: 152198 Hom.: 4112 Cov.: 32 AF XY: 0.184 AC XY: 13717 AN XY: 74416

African (AFR) AF: 0.412 AC: 17079 AN: 41504

American (AMR) AF: 0.111 AC: 1694 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 272 AN: 3462

East Asian (EAS) AF: 0.0935 AC: 485 AN: 5188

South Asian (SAS) AF: 0.0739 AC: 357 AN: 4828

European-Finnish (FIN) AF: 0.0988 AC: 1046 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7291 AN: 68012

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.125 Hom.: 2681

Bravo AF: 0.200

Asia WGS AF: 0.110 AC: 383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs4431886; hg19: chr1-56852267;