chr1-100747693-C-A

Variant names:

• chr1-100747693-C-A
• rs6660837
• ENST00000762830.1:n.85-11940G>T

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.85-11940G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,454 control chromosomes in the GnomAD database, including 7,266 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 0.30 (7266 hom., cov: 30)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800
• Publications: 6 publications found

Genes affected

ENSG00000299357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762830.1. 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
	ENSG00000299357	ENST00000762830.1		n.85-11940G>T		intron	N/A
	ENSG00000299373	ENST00000762919.1		n.-196C>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45786 AN: 151334 Hom.: 7263 Cov.: 30

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.302 AC: 45806 AN: 151454 Hom.: 7266 Cov.: 30 AF XY: 0.306 AC XY: 22633 AN XY: 73992

African (AFR) AF: 0.387 AC: 15983 AN: 41266

American (AMR) AF: 0.325 AC: 4944 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1274 AN: 5144

South Asian (SAS) AF: 0.358 AC: 1724 AN: 4812

European-Finnish (FIN) AF: 0.287 AC: 2971 AN: 10366

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17448 AN: 67878

Other (OTH) AF: 0.279 AC: 587 AN: 2104

Alfa AF: 0.268 Hom.: 7852

Bravo AF: 0.307

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.57
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs6660837; hg19: chr1-101213249;