rs6464104

Variant names:

• chr7-150781315-C-T
• rs6464104
• ENST00000745635.1:n.299-515G>A

Variant summary

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

The ENST00000745635.1(ENSG00000289470):​n.299-515G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,066 control chromosomes in the GnomAD database, including 38,432 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 0.70 (38432 hom., cov: 31)
• Consequence: ENSG00000289470 ENST00000745635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 12 publications found

Genes affected

ENSG00000289470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375566	XR_001745423.2	n.81-515G>A		intron_variant	Intron 1 of 3
LOC105375566	XR_001745422.2	n.-186G>A		upstream_gene_variant
LOC105375566	XR_001745424.2	n.-186G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289470	ENST00000745635.1	n.299-515G>A		intron_variant	Intron 1 of 2
ENSG00000289470	ENST00000745637.1	n.106-515G>A		intron_variant	Intron 1 of 3
ENSG00000289470	ENST00000745638.1	n.81-515G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106796 AN: 151948 Hom.: 38392 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 106896 AN: 152066 Hom.: 38432 Cov.: 31 AF XY: 0.698 AC XY: 51869 AN XY: 74318

African (AFR) AF: 0.857 AC: 35561 AN: 41490

American (AMR) AF: 0.696 AC: 10648 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2570 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3217 AN: 5160

South Asian (SAS) AF: 0.690 AC: 3323 AN: 4814

European-Finnish (FIN) AF: 0.557 AC: 5877 AN: 10560

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43448 AN: 67966

Other (OTH) AF: 0.726 AC: 1534 AN: 2112

Alfa AF: 0.680 Hom.: 6236

Bravo AF: 0.718

Asia WGS AF: 0.676 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.72
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs6464104; hg19: chr7-150478403;