chr1-84760616-T-C

Variant names:

• chr1-84760616-T-C
• rs1750491
• ENST00000813014.1:n.148+624T>C

Variant summary

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

The ENST00000813014.1(ENSG00000305800):​n.148+624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,108 control chromosomes in the GnomAD database, including 38,308 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 0.71 (38308 hom., cov: 33)
• Consequence: ENSG00000305800 ENST00000813014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 4 publications found

Genes affected

ENSG00000305800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813014.1. 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
	ENSG00000305800	ENST00000813014.1		n.148+624T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107357 AN: 151990 Hom.: 38297 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.706 AC: 107415 AN: 152108 Hom.: 38308 Cov.: 33 AF XY: 0.711 AC XY: 52879 AN XY: 74346

African (AFR) AF: 0.611 AC: 25336 AN: 41466

American (AMR) AF: 0.730 AC: 11161 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2585 AN: 3472

East Asian (EAS) AF: 0.763 AC: 3955 AN: 5182

South Asian (SAS) AF: 0.662 AC: 3193 AN: 4822

European-Finnish (FIN) AF: 0.831 AC: 8791 AN: 10576

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49904 AN: 67982

Other (OTH) AF: 0.720 AC: 1521 AN: 2112

Alfa AF: 0.709 Hom.: 31823

Bravo AF: 0.700

Asia WGS AF: 0.725 AC: 2519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	10
DANN	Benign	0.91
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1750491; hg19: chr1-85226299;