chr6-27192316-A-G

Variant names:

• chr6-27192316-A-G
• rs1102563
• ENST00000748463.1:n.64+4130A>G

Variant summary

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

The ENST00000748463.1(ENSG00000297504):​n.64+4130A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,964 control chromosomes in the GnomAD database, including 31,363 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 0.61 (31363 hom., cov: 31)
• Consequence: ENSG00000297504 ENST00000748463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• Publications: 5 publications found

Genes affected

ENSG00000297504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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
ENSG00000297504	ENST00000748463.1	n.64+4130A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92037 AN: 151846 Hom.: 31358 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.606 AC: 92055 AN: 151964 Hom.: 31363 Cov.: 31 AF XY: 0.603 AC XY: 44758 AN XY: 74258

African (AFR) AF: 0.273 AC: 11313 AN: 41430

American (AMR) AF: 0.667 AC: 10189 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2498 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3800 AN: 5154

South Asian (SAS) AF: 0.703 AC: 3386 AN: 4814

European-Finnish (FIN) AF: 0.645 AC: 6799 AN: 10542

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51967 AN: 67964

Other (OTH) AF: 0.605 AC: 1278 AN: 2114

Alfa AF: 0.717 Hom.: 66442

Bravo AF: 0.590

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.72
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1102563; hg19: chr6-27160095;