6-82264372-G-T

Variant names:

• chr6-82264372-G-T
• rs12664788
• ENST00000401636.1:n.603C>A

Variant summary

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

The ENST00000401636.1(ENSG00000220537):​n.603C>A 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 0.1 in 441,436 control chromosomes in the GnomAD database, including 3,260 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 0.13 (1792 hom., cov: 32)
  • Exomes 𝑓: 0.086 (1468 hom.)
• Consequence: ENSG00000220537 ENST00000401636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 5 publications found

Genes affected

ENSG00000220537 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000401636.1. 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
	ENSG00000220537	ENST00000401636.1	TSL:6	n.603C>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19521 AN: 152018 Hom.: 1795 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0856 AC: 24770 AN: 289300 Hom.: 1468 Cov.: 0 AF XY: 0.0849 AC XY: 13818 AN XY: 162722

African (AFR) AF: 0.246 AC: 2020 AN: 8202

American (AMR) AF: 0.113 AC: 2820 AN: 24930

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 492 AN: 6850

East Asian (EAS) AF: 0.186 AC: 2073 AN: 11160

South Asian (SAS) AF: 0.0956 AC: 4783 AN: 50034

European-Finnish (FIN) AF: 0.111 AC: 3031 AN: 27332

Middle Eastern (MID) AF: 0.165 AC: 229 AN: 1392

European-Non Finnish (NFE) AF: 0.0561 AC: 8227 AN: 146614

Other (OTH) AF: 0.0856 AC: 1095 AN: 12786

GnomAD4 genome AF: 0.128 AC: 19533 AN: 152136 Hom.: 1792 Cov.: 32 AF XY: 0.132 AC XY: 9822 AN XY: 74380

African (AFR) AF: 0.246 AC: 10201 AN: 41468

American (AMR) AF: 0.141 AC: 2151 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0730 AC: 253 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5172

South Asian (SAS) AF: 0.0966 AC: 465 AN: 4814

European-Finnish (FIN) AF: 0.117 AC: 1234 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0567 AC: 3854 AN: 68016

Other (OTH) AF: 0.142 AC: 300 AN: 2116

Alfa AF: 0.0819 Hom.: 2977

Bravo AF: 0.134

Asia WGS AF: 0.147 AC: 510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	4.3
DANN	Benign	0.76
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs12664788; hg19: chr6-82974089;