chr6-91332186-A-C

Variant names:

• chr6-91332186-A-C
• rs2144363
• ENST00000736553.1:n.89-4080T>G

Variant summary

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

The ENST00000736553.1(ENSG00000296122):​n.89-4080T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 151,916 control chromosomes in the GnomAD database, including 941 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 0.091 (941 hom., cov: 32)
• Consequence: ENSG00000296122 ENST00000736553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 7 publications found

Genes affected

ENSG00000296122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000736553.1. 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
	ENSG00000296122	ENST00000736553.1		n.89-4080T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13819 AN: 151798 Hom.: 940 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0365

Gnomad OTH AF: 0.0840

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

GnomAD4 genome AF: 0.0911 AC: 13834 AN: 151916 Hom.: 941 Cov.: 32 AF XY: 0.0933 AC XY: 6921 AN XY: 74214

African (AFR) AF: 0.165 AC: 6852 AN: 41410

American (AMR) AF: 0.0895 AC: 1364 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1499 AN: 5112

South Asian (SAS) AF: 0.148 AC: 708 AN: 4796

European-Finnish (FIN) AF: 0.0214 AC: 227 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0365 AC: 2482 AN: 67984

Other (OTH) AF: 0.0865 AC: 183 AN: 2116

Alfa AF: 0.0532 Hom.: 1070

Bravo AF: 0.104

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.55
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2144363; hg19: chr6-92041904;