6-127106973-T-C

Variant names:

• chr6-127106973-T-C
• rs1936795
• ENST00000650648.1:n.402-35887A>G

Variant summary

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

The ENST00000650648.1(ENSG00000293110):​n.402-35887A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,048 control chromosomes in the GnomAD database, including 10,193 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 0.36 (10193 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 2 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650648.1		n.402-35887A>G		intron	N/A
	ENSG00000293110	ENST00000650684.1		n.474-35887A>G		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.441-35887A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54148 AN: 151928 Hom.: 10179 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.356 AC: 54204 AN: 152048 Hom.: 10193 Cov.: 32 AF XY: 0.358 AC XY: 26618 AN XY: 74318

African (AFR) AF: 0.451 AC: 18705 AN: 41466

American (AMR) AF: 0.383 AC: 5855 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1187 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2813 AN: 5170

South Asian (SAS) AF: 0.369 AC: 1775 AN: 4814

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10562

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19888 AN: 67976

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.332 Hom.: 3376

Bravo AF: 0.374

Asia WGS AF: 0.428 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.22
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1936795; hg19: chr6-127428118;