1-169630994-T-C

Variant names:

• chr1-169630994-T-C
• rs3753306

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 0.231 in 152,184 control chromosomes in the GnomAD database, including 6,573 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 0.23 (6573 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 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: 0.231 AC: 35110 AN: 152066 Hom.: 6543 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.231 AC: 35195 AN: 152184 Hom.: 6573 Cov.: 33 AF XY: 0.231 AC XY: 17211 AN XY: 74416

African (AFR) AF: 0.520 AC: 21559 AN: 41480

American (AMR) AF: 0.190 AC: 2910 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.139 AC: 719 AN: 5186

South Asian (SAS) AF: 0.132 AC: 635 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1400 AN: 10604

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7080 AN: 68024

Other (OTH) AF: 0.192 AC: 407 AN: 2116

Alfa AF: 0.147 Hom.: 1486

Bravo AF: 0.248

Asia WGS AF: 0.153 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.52
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3753306; hg19: chr1-169600232;