rs13340508

Variant names:

• chr7-75808367-T-C
• rs13340508

Your query was ambiguous. Multiple possible variants found:

• chr7-75808367-T-C
• chr7-75808367-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 0.211 in 152,114 control chromosomes in the GnomAD database, including 3,515 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 0.21 (3515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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: 0.211 AC: 32015 AN: 151996 Hom.: 3508 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.211 AC: 32031 AN: 152114 Hom.: 3515 Cov.: 32 AF XY: 0.216 AC XY: 16071 AN XY: 74340

African (AFR) AF: 0.194 AC: 8051 AN: 41508

American (AMR) AF: 0.279 AC: 4255 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1653 AN: 5168

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4822

European-Finnish (FIN) AF: 0.277 AC: 2933 AN: 10574

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

European-Non Finnish (NFE) AF: 0.185 AC: 12605 AN: 67984

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.195 Hom.: 10868

Bravo AF: 0.211

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.094
DANN	Benign	0.41
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs13340508; hg19: chr7-75437685;