6-98048076-A-G

Variant names:

• chr6-98048076-A-G
• rs2505059
• ENST00000606913.5:n.156-51110A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000607032.1(ENSG00000271860):​n.247-27991A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,814 control chromosomes in the GnomAD database, including 20,576 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 0.52 (20576 hom., cov: 31)
• Consequence: ENSG00000271860 ENST00000607032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 11 publications found

Genes affected

ENSG00000271860 (HGNC:58964):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607032.1. 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
	ENSG00000271860	ENST00000606913.5	TSL:5	n.156-51110A>G		intron	N/A
	ENSG00000271860	ENST00000607032.1	TSL:3	n.247-27991A>G		intron	N/A
	ENSG00000271860	ENST00000607823.5	TSL:5	n.268-51110A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78436 AN: 151696 Hom.: 20545 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.517 AC: 78528 AN: 151814 Hom.: 20576 Cov.: 31 AF XY: 0.522 AC XY: 38688 AN XY: 74180

African (AFR) AF: 0.585 AC: 24205 AN: 41396

American (AMR) AF: 0.500 AC: 7606 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1682 AN: 3464

East Asian (EAS) AF: 0.353 AC: 1812 AN: 5140

South Asian (SAS) AF: 0.629 AC: 3028 AN: 4812

European-Finnish (FIN) AF: 0.564 AC: 5938 AN: 10536

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32512 AN: 67936

Other (OTH) AF: 0.514 AC: 1082 AN: 2104

Alfa AF: 0.488 Hom.: 72526

Bravo AF: 0.509

Asia WGS AF: 0.528 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	12
DANN	Benign	0.58
PhyloP100		0.87

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: rs2505059;

hg19: chr6-98495952;