rs12210810

Variant names:

• chr6-118332041-G-C
• rs12210810
• ENST00000778490.1:n.618-30708C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-118332041-G-C
• chr6-118332041-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000778490.1(ENSG00000301363):​n.618-30708C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 152,308 control chromosomes in the GnomAD database, including 147 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 0.036 (147 hom., cov: 33)
• Consequence: ENSG00000301363 ENST00000778490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 34 publications found

Genes affected

ENSG00000301363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778490.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301363	ENST00000778490.1		n.618-30708C>G		intron	N/A
	ENSG00000301363	ENST00000778491.1		n.159-6854C>G		intron	N/A
	ENSG00000301363	ENST00000778492.1		n.622-7858C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5446 AN: 152190 Hom.: 148 Cov.: 33

Gnomad AFR AF: 0.00955

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0356

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0534

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0357 AC: 5442 AN: 152308 Hom.: 147 Cov.: 33 AF XY: 0.0354 AC XY: 2636 AN XY: 74466

African (AFR) AF: 0.00952 AC: 396 AN: 41576

American (AMR) AF: 0.0270 AC: 413 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4822

European-Finnish (FIN) AF: 0.0356 AC: 378 AN: 10610

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0534 AC: 3632 AN: 68026

Other (OTH) AF: 0.0402 AC: 85 AN: 2114

Alfa AF: 0.0448 Hom.: 108

Bravo AF: 0.0326

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12210810;

hg19: chr6-118653204;