chr1-24968387-T-C

Variant names:

• chr1-24968387-T-C
• rs10903118
• ENST00000568143.1:n.*36A>G

Variant summary

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

The ENST00000568143.1(ENSG00000261025):​n.*36A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,018 control chromosomes in the GnomAD database, including 18,534 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 0.48 (18533 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENSG00000261025 ENST00000568143.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 26 publications found

Genes affected

ENSG00000261025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568143.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261025	ENST00000568143.1	TSL:6	n.*36A>G		downstream_gene	N/A
	ENSG00000261025	ENST00000751467.1		n.*34A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72219 AN: 151896 Hom.: 18506 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.475 AC: 72266 AN: 152014 Hom.: 18533 Cov.: 31 AF XY: 0.491 AC XY: 36453 AN XY: 74306

African (AFR) AF: 0.287 AC: 11893 AN: 41458

American (AMR) AF: 0.640 AC: 9774 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1764 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3663 AN: 5178

South Asian (SAS) AF: 0.671 AC: 3232 AN: 4818

European-Finnish (FIN) AF: 0.575 AC: 6067 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34004 AN: 67960

Other (OTH) AF: 0.514 AC: 1082 AN: 2106

Alfa AF: 0.503 Hom.: 34206

Bravo AF: 0.473

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.61
PhyloP100		-2.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10903118; hg19: chr1-25294878;