rs12111385

chr6-8370534-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670476.1(ENSG00000234763):n.228+8205A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 148,170 control chromosomes in the GnomAD database, including 4,253 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 0.24 (4253 hom., cov: 27)
• Consequence: ENST00000670476.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.1).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670476.1	n.228+8205A>G		intron_variant, non_coding_transcript_variant
	ENST00000651914.1	n.160-2118A>G		intron_variant, non_coding_transcript_variant
	ENST00000655767.1	n.229-7702A>G		intron_variant, non_coding_transcript_variant
	ENST00000661402.1	n.424+18226A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 35247 AN: 148080 Hom.: 4251 Cov.: 27

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.238 AC: 35266 AN: 148170 Hom.: 4253 Cov.: 27 AF XY: 0.232 AC XY: 16738 AN XY: 72018

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.251

Alfa AF: 0.252 Hom.: 619

Bravo AF: 0.236

Asia WGS AF: 0.144 AC: 504 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.12
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12111385; hg19: chr6-8370767;