rs7068685

Variant names:

• chr10-5114472-A-G
• rs7068685

Your query was ambiguous. Multiple possible variants found:

• chr10-5114472-A-G
• chr10-5114472-A-T

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 0.25 in 152,132 control chromosomes in the GnomAD database, including 4,905 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 0.25 (4905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 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: 0.250 AC: 37994 AN: 152016 Hom.: 4891 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.250 AC: 38038 AN: 152132 Hom.: 4905 Cov.: 32 AF XY: 0.247 AC XY: 18369 AN XY: 74370

African (AFR) AF: 0.286 AC: 11877 AN: 41494

American (AMR) AF: 0.230 AC: 3510 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 915 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1219 AN: 5164

South Asian (SAS) AF: 0.205 AC: 988 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10578

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16080 AN: 67998

Other (OTH) AF: 0.296 AC: 625 AN: 2110

Alfa AF: 0.242 Hom.: 1268

Bravo AF: 0.255

Asia WGS AF: 0.260 AC: 902 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7068685; hg19: chr10-5156664;