chr1-209874273-T-C

Variant names:

• chr1-209874273-T-C
• rs1319435

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 0.106 in 152,234 control chromosomes in the GnomAD database, including 1,134 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 (1134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 6 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.151 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

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16168 AN: 152116 Hom.: 1136 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0437

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.106 AC: 16162 AN: 152234 Hom.: 1134 Cov.: 32 AF XY: 0.104 AC XY: 7725 AN XY: 74422

African (AFR) AF: 0.0313 AC: 1301 AN: 41560

American (AMR) AF: 0.108 AC: 1655 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5184

South Asian (SAS) AF: 0.150 AC: 724 AN: 4812

European-Finnish (FIN) AF: 0.110 AC: 1168 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10445 AN: 67994

Other (OTH) AF: 0.105 AC: 221 AN: 2114

Alfa AF: 0.124 Hom.: 611

Bravo AF: 0.100

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.82
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1319435; hg19: chr1-210047618;