1-207749736-A-G

Variant names:

• chr1-207749736-A-G
• rs2761437
• ENST00000830828.1:n.464+1749T>C

Variant summary

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

The ENST00000830828.1(ENSG00000308069):​n.464+1749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,148 control chromosomes in the GnomAD database, including 48,541 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 0.80 (48541 hom., cov: 32)
• Consequence: ENSG00000308069 ENST00000830828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 17 publications found

Genes affected

ENSG00000308069 (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 = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830828.1. 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
	ENSG00000308069	ENST00000830828.1		n.464+1749T>C		intron	N/A
	ENSG00000308069	ENST00000830829.1		n.283+1749T>C		intron	N/A
	ENSG00000308069	ENST00000830830.1		n.344+1749T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121287 AN: 152030 Hom.: 48483 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.798 AC: 121396 AN: 152148 Hom.: 48541 Cov.: 32 AF XY: 0.799 AC XY: 59456 AN XY: 74374

African (AFR) AF: 0.798 AC: 33102 AN: 41492

American (AMR) AF: 0.753 AC: 11502 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3015 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5150 AN: 5184

South Asian (SAS) AF: 0.854 AC: 4114 AN: 4820

European-Finnish (FIN) AF: 0.780 AC: 8249 AN: 10576

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53464 AN: 68004

Other (OTH) AF: 0.828 AC: 1747 AN: 2110

Alfa AF: 0.790 Hom.: 92186

Bravo AF: 0.794

Asia WGS AF: 0.917 AC: 3188 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	1.8
DANN	Benign	0.49
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2761437; hg19: chr1-207923081;