rs4075570

Variant names:

• chr6-77194092-G-A
• rs4075570
• ENST00000790532.1:n.437-42812C>T

Variant summary

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

The ENST00000790532.1(ENSG00000302932):​n.437-42812C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,892 control chromosomes in the GnomAD database, including 27,565 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 0.60 (27565 hom., cov: 33)
• Consequence: ENSG00000302932 ENST00000790532.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 12 publications found

Genes affected

ENSG00000302932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928570	XR_001744205.2	n.1271-42118C>T		intron_variant	Intron 3 of 4
LOC101928570	XR_001744206.2	n.1346+17889C>T		intron_variant	Intron 4 of 5
LOC101928570	XR_001744207.2	n.1271-42812C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302932	ENST00000790532.1	n.437-42812C>T		intron_variant	Intron 2 of 5
ENSG00000302932	ENST00000790533.1	n.550-42118C>T		intron_variant	Intron 3 of 6
ENSG00000302932	ENST00000790534.1	n.682-42118C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90605 AN: 151774 Hom.: 27567 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.597 AC: 90652 AN: 151892 Hom.: 27565 Cov.: 33 AF XY: 0.597 AC XY: 44326 AN XY: 74254

African (AFR) AF: 0.486 AC: 20136 AN: 41454

American (AMR) AF: 0.663 AC: 10099 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3190 AN: 5162

South Asian (SAS) AF: 0.569 AC: 2740 AN: 4814

European-Finnish (FIN) AF: 0.662 AC: 7005 AN: 10578

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42840 AN: 67878

Other (OTH) AF: 0.633 AC: 1332 AN: 2104

Alfa AF: 0.611 Hom.: 20981

Bravo AF: 0.593

Asia WGS AF: 0.608 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.72
DANN	Benign	0.55
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs4075570; hg19: chr6-77903809;