rs768586

Variant names:

• chr1-34709225-T-C
• rs768586

Your query was ambiguous. Multiple possible variants found:

• chr1-34709225-T-C
• chr1-34709225-T-G

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 0.186 in 152,092 control chromosomes in the GnomAD database, including 2,951 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 0.19 (2951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 1 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 = 0.236 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: 0.186 AC: 28236 AN: 151974 Hom.: 2948 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.186 AC: 28258 AN: 152092 Hom.: 2951 Cov.: 32 AF XY: 0.185 AC XY: 13735 AN XY: 74358

African (AFR) AF: 0.0892 AC: 3701 AN: 41496

American (AMR) AF: 0.167 AC: 2556 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 969 AN: 3470

East Asian (EAS) AF: 0.116 AC: 602 AN: 5180

South Asian (SAS) AF: 0.101 AC: 489 AN: 4824

European-Finnish (FIN) AF: 0.283 AC: 2998 AN: 10578

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16278 AN: 67958

Other (OTH) AF: 0.188 AC: 398 AN: 2116

Alfa AF: 0.166 Hom.: 567

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.64
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs768586; hg19: chr1-35174826;