rs612399

Variant names:

• chr6-41320065-T-C
• rs612399
• ENST00000815698.1:n.750T>C

Variant summary

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

The ENST00000815698.1(ENSG00000306154):​n.750T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,178 control chromosomes in the GnomAD database, including 9,099 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 0.34 (9099 hom., cov: 33)
• Consequence: ENSG00000306154 ENST00000815698.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 6 publications found

Genes affected

ENSG00000306154 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815698.1. 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
	ENSG00000306154	ENST00000815698.1		n.750T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000306154	ENST00000815699.1		n.426-58T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51454 AN: 152058 Hom.: 9090 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.338 AC: 51495 AN: 152178 Hom.: 9099 Cov.: 33 AF XY: 0.340 AC XY: 25291 AN XY: 74412

African (AFR) AF: 0.246 AC: 10211 AN: 41524

American (AMR) AF: 0.274 AC: 4188 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2470 AN: 5174

South Asian (SAS) AF: 0.483 AC: 2327 AN: 4820

European-Finnish (FIN) AF: 0.406 AC: 4301 AN: 10600

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25607 AN: 67986

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.361 Hom.: 35995

Bravo AF: 0.323

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.83
PhyloP100		0.0060

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: rs612399;

hg19: chr6-41287803;