rs3218114

Variant names:

• chr6-41934614-C-T
• rs3218114

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 0.158 in 152,194 control chromosomes in the GnomAD database, including 2,005 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 0.16 (2005 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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: 0.158 AC: 23961 AN: 152076 Hom.: 2003 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.158 AC: 23976 AN: 152194 Hom.: 2005 Cov.: 33 AF XY: 0.160 AC XY: 11877 AN XY: 74392

African (AFR) AF: 0.109 AC: 4535 AN: 41544

American (AMR) AF: 0.141 AC: 2149 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0983 AC: 341 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1309 AN: 5180

South Asian (SAS) AF: 0.215 AC: 1040 AN: 4826

European-Finnish (FIN) AF: 0.192 AC: 2024 AN: 10568

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12074 AN: 68004

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.146 Hom.: 365

Bravo AF: 0.153

Asia WGS AF: 0.216 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.1
DANN	Benign	0.78
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3218114; hg19: chr6-41902352;