6-91819995-T-G

Variant names:

• chr6-91819995-T-G
• rs1498249
• ENST00000785449.1:n.663+3324T>G

Variant summary

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

The ENST00000785449.1(ENSG00000302276):​n.663+3324T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,044 control chromosomes in the GnomAD database, including 2,818 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 0.19 (2818 hom., cov: 32)
• Consequence: ENSG00000302276 ENST00000785449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 1 publications found

Genes affected

ENSG00000302276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302276	ENST00000785449.1	n.663+3324T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28478 AN: 151924 Hom.: 2811 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.188 AC: 28510 AN: 152044 Hom.: 2818 Cov.: 32 AF XY: 0.195 AC XY: 14527 AN XY: 74322

African (AFR) AF: 0.203 AC: 8424 AN: 41466

American (AMR) AF: 0.131 AC: 1999 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1053 AN: 5138

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4812

European-Finnish (FIN) AF: 0.290 AC: 3066 AN: 10582

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11741 AN: 67984

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.164 Hom.: 1223

Bravo AF: 0.174

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.73
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1498249; hg19: chr6-92529713;