rs3936080

Positions:

• chr6-120537607-T-C

Variant summary

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

The ENST00000657887.1(ENSG00000286540):​n.81+75016T>C 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 0.39 in 151,894 control chromosomes in the GnomAD database, including 12,639 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 0.39 (12639 hom., cov: 31)
• Consequence: ENST00000657887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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
	ENST00000657887.1	n.81+75016T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59272 AN: 151774 Hom.: 12640 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.390 AC: 59289 AN: 151894 Hom.: 12639 Cov.: 31 AF XY: 0.389 AC XY: 28849 AN XY: 74220

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.417

Alfa AF: 0.430 Hom.: 3934

Bravo AF: 0.386

Asia WGS AF: 0.372 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3936080; hg19: chr6-120858753;