chr1-203291628-A-G

Variant names:

• chr1-203291628-A-G
• rs7530895
• ENST00000779926.1:n.*247A>G

Variant summary

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

The ENST00000779926.1(ENSG00000301574):​n.*247A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,056 control chromosomes in the GnomAD database, including 7,557 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 0.21 (7557 hom., cov: 32)
• Consequence: ENSG00000301574 ENST00000779926.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 5 publications found

Genes affected

ENSG00000301574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779926.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301574	ENST00000779926.1		n.*247A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31769 AN: 151938 Hom.: 7526 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0326

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.209 AC: 31846 AN: 152056 Hom.: 7557 Cov.: 32 AF XY: 0.208 AC XY: 15483 AN XY: 74332

African (AFR) AF: 0.569 AC: 23558 AN: 41424

American (AMR) AF: 0.127 AC: 1939 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3468

East Asian (EAS) AF: 0.385 AC: 1992 AN: 5168

South Asian (SAS) AF: 0.154 AC: 745 AN: 4826

European-Finnish (FIN) AF: 0.0473 AC: 501 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0326 AC: 2214 AN: 67988

Other (OTH) AF: 0.177 AC: 372 AN: 2096

Alfa AF: 0.0976 Hom.: 5007

Bravo AF: 0.232

Asia WGS AF: 0.270 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.67
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs7530895; hg19: chr1-203260756;