1-42048781-T-C

Variant names:

• chr1-42048781-T-C
• rs11210568
• ENST00000670076.1:n.495+58T>C

Variant summary

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

The ENST00000670076.1(ENSG00000287587):​n.495+58T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,956 control chromosomes in the GnomAD database, including 9,904 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 0.34 (9904 hom., cov: 31)
• Consequence: ENSG00000287587 ENST00000670076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728
• Publications: 2 publications found

Genes affected

ENSG00000287587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904161	XR_007066032.1	n.168+58T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287587	ENST00000670076.1	n.495+58T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50908 AN: 151836 Hom.: 9905 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.335 AC: 50908 AN: 151956 Hom.: 9904 Cov.: 31 AF XY: 0.330 AC XY: 24519 AN XY: 74262

African (AFR) AF: 0.144 AC: 5989 AN: 41456

American (AMR) AF: 0.310 AC: 4729 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1687 AN: 3464

East Asian (EAS) AF: 0.491 AC: 2537 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4806

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10540

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29862 AN: 67952

Other (OTH) AF: 0.365 AC: 769 AN: 2106

Alfa AF: 0.404 Hom.: 22007

Bravo AF: 0.329

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.39
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11210568; hg19: chr1-42514452;