chr1-60424002-G-A

Variant names:

• chr1-60424002-G-A
• rs1501241
• ENST00000794751.1:n.393-30104C>T

Variant summary

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

The ENST00000794751.1(ENSG00000303463):​n.393-30104C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 151,966 control chromosomes in the GnomAD database, including 1,004 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 0.069 (1004 hom., cov: 32)
• Consequence: ENSG00000303463 ENST00000794751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 2 publications found

Genes affected

ENSG00000303463 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794751.1. 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
	ENSG00000303463	ENST00000794751.1		n.393-30104C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10390 AN: 151850 Hom.: 1002 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.00924

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.0714

Gnomad FIN AF: 0.00322

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00615

Gnomad OTH AF: 0.0503

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

GnomAD4 genome AF: 0.0685 AC: 10410 AN: 151966 Hom.: 1004 Cov.: 32 AF XY: 0.0681 AC XY: 5057 AN XY: 74284

African (AFR) AF: 0.207 AC: 8554 AN: 41400

American (AMR) AF: 0.0389 AC: 594 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00924 AC: 32 AN: 3464

East Asian (EAS) AF: 0.0562 AC: 291 AN: 5176

South Asian (SAS) AF: 0.0719 AC: 345 AN: 4798

European-Finnish (FIN) AF: 0.00322 AC: 34 AN: 10568

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00615 AC: 418 AN: 67988

Other (OTH) AF: 0.0507 AC: 107 AN: 2110

Alfa AF: 0.0309 Hom.: 139

Bravo AF: 0.0764

Asia WGS AF: 0.0780 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.3
DANN	Benign	0.48
PhyloP100		0.40

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: rs1501241;

hg19: chr1-60889674;