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 ENST00000801152.1(ENSG00000260000):​n.522A>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: ENSG00000260000 ENST00000801152.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801152.1. 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
	ENSG00000270987	ENST00000604292.1	TSL:6	n.133A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000260000	ENST00000801152.1		n.522A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000260000	ENST00000801153.1		n.527A>G		non_coding_transcript_exon	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 v4.9

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;