chr1-170352171-T-C

Variant names:

• chr1-170352171-T-C
• rs10919359

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 0.434 in 151,804 control chromosomes in the GnomAD database, including 15,126 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 0.43 (15126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65794 AN: 151686 Hom.: 15092 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.434 AC: 65887 AN: 151804 Hom.: 15126 Cov.: 32 AF XY: 0.443 AC XY: 32839 AN XY: 74178

African (AFR) AF: 0.497 AC: 20575 AN: 41420

American (AMR) AF: 0.425 AC: 6463 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1170 AN: 3462

East Asian (EAS) AF: 0.786 AC: 4038 AN: 5136

South Asian (SAS) AF: 0.597 AC: 2879 AN: 4820

European-Finnish (FIN) AF: 0.429 AC: 4515 AN: 10536

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25097 AN: 67900

Other (OTH) AF: 0.413 AC: 870 AN: 2106

Alfa AF: 0.399 Hom.: 5377

Bravo AF: 0.435

Asia WGS AF: 0.678 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10919359; hg19: chr1-170321312;