chr6-85014445-T-A

Variant names:

• chr6-85014445-T-A
• rs6919160
• ENST00000805044.1:n.225-2534T>A

Variant summary

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

The ENST00000805044.1(ENSG00000304631):​n.225-2534T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,840 control chromosomes in the GnomAD database, including 11,979 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 (11979 hom., cov: 31)
• Consequence: ENSG00000304631 ENST00000805044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 2 publications found

Genes affected

ENSG00000304631 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805044.1. 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
	ENSG00000304631	ENST00000805044.1		n.225-2534T>A		intron	N/A
	ENSG00000304631	ENST00000805045.1		n.141-2534T>A		intron	N/A
	ENSG00000304631	ENST00000805046.1		n.142-1693T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58725 AN: 151722 Hom.: 11966 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.387 AC: 58787 AN: 151840 Hom.: 11979 Cov.: 31 AF XY: 0.398 AC XY: 29546 AN XY: 74232

African (AFR) AF: 0.460 AC: 19023 AN: 41392

American (AMR) AF: 0.482 AC: 7359 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3466

East Asian (EAS) AF: 0.528 AC: 2714 AN: 5144

South Asian (SAS) AF: 0.509 AC: 2453 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4309 AN: 10532

Middle Eastern (MID) AF: 0.310 AC: 90 AN: 290

European-Non Finnish (NFE) AF: 0.302 AC: 20540 AN: 67904

Other (OTH) AF: 0.365 AC: 769 AN: 2108

Alfa AF: 0.215 Hom.: 465

Bravo AF: 0.393

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6919160; hg19: chr6-85724163;