6-100889735-A-G

Variant names:

• chr6-100889735-A-G
• rs9498419
• ENST00000604292.1:n.133A>G

Variant summary

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

The ENST00000604292.1(ENSG00000270987):​n.133A>G 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 0.523 in 1,613,470 control chromosomes in the GnomAD database, including 224,165 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 0.51 (20476 hom., cov: 33)
  • Exomes 𝑓: 0.52 (203689 hom.)
• Consequence: ENSG00000270987 ENST00000604292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 6 publications found

Genes affected

ENSG00000270987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC728098		n.100889735A>G		intragenic_variant
LOC107984041	XR_002956381.2	n.199-2263A>G		intron_variant	Intron 1 of 6
LOC107984041	XR_002956382.2	n.199-2263A>G		intron_variant	Intron 1 of 3
LOC107984041	XR_007059692.1	n.199-2263A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270987	ENST00000604292.1	n.133A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000260000	ENST00000801152.1	n.522A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000260000	ENST00000801153.1	n.527A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000260000	ENST00000801154.1	n.528A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78190 AN: 151880 Hom.: 20447 Cov.: 33

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.532

GnomAD4 exome AF: 0.524 AC: 765918 AN: 1461472 Hom.: 203689 Cov.: 47 AF XY: 0.519 AC XY: 377643 AN XY: 727052

African (AFR) AF: 0.441 AC: 14774 AN: 33478

American (AMR) AF: 0.650 AC: 29052 AN: 44694

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 13822 AN: 26126

East Asian (EAS) AF: 0.780 AC: 30956 AN: 39700

South Asian (SAS) AF: 0.387 AC: 33351 AN: 86236

European-Finnish (FIN) AF: 0.509 AC: 27173 AN: 53408

Middle Eastern (MID) AF: 0.553 AC: 3190 AN: 5768

European-Non Finnish (NFE) AF: 0.524 AC: 582044 AN: 1111682

Other (OTH) AF: 0.523 AC: 31556 AN: 60380

GnomAD4 genome AF: 0.515 AC: 78265 AN: 151998 Hom.: 20476 Cov.: 33 AF XY: 0.514 AC XY: 38190 AN XY: 74324

African (AFR) AF: 0.452 AC: 18737 AN: 41452

American (AMR) AF: 0.611 AC: 9346 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1837 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3858 AN: 5158

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4808

European-Finnish (FIN) AF: 0.515 AC: 5447 AN: 10584

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35348 AN: 67932

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.511 Hom.: 3206

Bravo AF: 0.527

Asia WGS AF: 0.558 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.6
DANN	Benign	0.74
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9498419; hg19: chr6-101337611;