rs1041163

Variant names:

• chr1-100718269-T-C
• rs1041163
• ENST00000762830.1:n.154+17415A>G

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.154+17415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,134 control chromosomes in the GnomAD database, including 2,603 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 0.18 (2603 hom., cov: 32)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 49 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299357	ENST00000762830.1		n.154+17415A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26895 AN: 152016 Hom.: 2598 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.177 AC: 26914 AN: 152134 Hom.: 2603 Cov.: 32 AF XY: 0.176 AC XY: 13104 AN XY: 74364

African (AFR) AF: 0.181 AC: 7525 AN: 41510

American (AMR) AF: 0.274 AC: 4179 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 997 AN: 3472

East Asian (EAS) AF: 0.145 AC: 749 AN: 5160

South Asian (SAS) AF: 0.142 AC: 684 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1539 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10549 AN: 67986

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.168 Hom.: 9647

Bravo AF: 0.191

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1041163; hg19: chr1-101183825;