1-100768471-G-A

Variant names:

• chr1-100768471-G-A
• rs6702885
• ENST00000762830.1:n.84+13204C>T

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.84+13204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,894 control chromosomes in the GnomAD database, including 1,179 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 0.11 (1179 hom., cov: 31)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 3 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299357	ENST00000762830.1	n.84+13204C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16822 AN: 151776 Hom.: 1178 Cov.: 31

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.111 AC: 16820 AN: 151894 Hom.: 1179 Cov.: 31 AF XY: 0.109 AC XY: 8115 AN XY: 74258

African (AFR) AF: 0.0284 AC: 1178 AN: 41410

American (AMR) AF: 0.109 AC: 1665 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3466

East Asian (EAS) AF: 0.0901 AC: 466 AN: 5174

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4820

European-Finnish (FIN) AF: 0.174 AC: 1835 AN: 10540

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10520 AN: 67912

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0698 Hom.: 114

Bravo AF: 0.104

Asia WGS AF: 0.0550 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.32
DANN	Benign	0.70
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6702885; hg19: chr1-101234027; COSMIC: COSV59978374;