rs459162

Positions:

• chr6-1216141-G-A

Variant summary

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

The ENST00000700915.1(ENSG00000289842):​n.218+12250C>T 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 0.4 in 152,010 control chromosomes in the GnomAD database, including 13,045 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 0.40 (13045 hom., cov: 32)
• Consequence: ENST00000700915.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000700915.1	n.218+12250C>T		intron_variant, non_coding_transcript_variant
	ENST00000702015.1	n.218+12250C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60780 AN: 151892 Hom.: 13009 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.400 AC: 60872 AN: 152010 Hom.: 13045 Cov.: 32 AF XY: 0.402 AC XY: 29890 AN XY: 74308

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.398

Alfa AF: 0.339 Hom.: 18708

Bravo AF: 0.408

Asia WGS AF: 0.339 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs459162; hg19: chr6-1216376;