rs35130

Variant names:

• chr5-6007310-T-C
• rs35130

Your query was ambiguous. Multiple possible variants found:

• chr5-6007310-T-C
• chr5-6007310-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 0.971 in 152,308 control chromosomes in the GnomAD database, including 71,875 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 0.97 (71875 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.981 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: 0.971 AC: 147789 AN: 152188 Hom.: 71816 Cov.: 32

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.969

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

GnomAD4 genome AF: 0.971 AC: 147909 AN: 152308 Hom.: 71875 Cov.: 32 AF XY: 0.970 AC XY: 72227 AN XY: 74464

African (AFR) AF: 0.951 AC: 39501 AN: 41556

American (AMR) AF: 0.980 AC: 15004 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3402 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4532 AN: 5162

South Asian (SAS) AF: 0.990 AC: 4780 AN: 4830

European-Finnish (FIN) AF: 0.972 AC: 10326 AN: 10622

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67161 AN: 68038

Other (OTH) AF: 0.969 AC: 2048 AN: 2114

Alfa AF: 0.982 Hom.: 29971

Bravo AF: 0.969

Asia WGS AF: 0.944 AC: 3283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.33
DANN	Benign	0.41
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs35130; hg19: chr5-6007423;