1-196883651-T-C

Variant names:

• chr1-196883651-T-C
• rs10801575

Variant summary

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

The variant allele was found at a frequency of 0.594 in 150,192 control chromosomes in the GnomAD database, including 29,911 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 0.59 (29911 hom., cov: 29)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.753
• Publications: 16 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649395.1. 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
	ENSG00000285986	ENST00000649395.1		n.427-955T>C		intron	N/A
	ENSG00000304869	ENST00000806771.1		n.221+2818T>C		intron	N/A
	ENSG00000304869	ENST00000806772.1		n.416+2818T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 89114 AN: 150082 Hom.: 29892 Cov.: 29

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.594 AC: 89160 AN: 150192 Hom.: 29911 Cov.: 29 AF XY: 0.601 AC XY: 43994 AN XY: 73244

African (AFR) AF: 0.285 AC: 11615 AN: 40728

American (AMR) AF: 0.685 AC: 10264 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2188 AN: 3458

East Asian (EAS) AF: 0.818 AC: 4153 AN: 5076

South Asian (SAS) AF: 0.677 AC: 3233 AN: 4776

European-Finnish (FIN) AF: 0.809 AC: 8253 AN: 10200

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47304 AN: 67678

Other (OTH) AF: 0.594 AC: 1242 AN: 2090

Alfa AF: 0.675 Hom.: 33958

Bravo AF: 0.575

Asia WGS AF: 0.742 AC: 2579 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.46
PhyloP100		0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10801575; hg19: chr1-196852781;