chr6-41168112-C-T

Variant names:

• chr6-41168112-C-T
• rs7759295
• ENST00000702590.2:n.365-8775C>T

Variant summary

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

The ENST00000702590.2(ENSG00000290034):​n.365-8775C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 152,228 control chromosomes in the GnomAD database, including 728 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 0.090 (728 hom., cov: 32)
• Consequence: ENSG00000290034 ENST00000702590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 16 publications found

Genes affected

ENSG00000290034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000702590.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290034	ENST00000702590.2		n.365-8775C>T		intron	N/A
	ENSG00000290034	ENST00000736037.1		n.365-8781C>T		intron	N/A
	ENSG00000290034	ENST00000736038.1		n.363-8775C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13717 AN: 152110 Hom.: 728 Cov.: 32

Gnomad AFR AF: 0.0437

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0935

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

GnomAD4 genome AF: 0.0901 AC: 13720 AN: 152228 Hom.: 728 Cov.: 32 AF XY: 0.0871 AC XY: 6483 AN XY: 74410

African (AFR) AF: 0.0437 AC: 1816 AN: 41532

American (AMR) AF: 0.0770 AC: 1178 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3472

East Asian (EAS) AF: 0.0489 AC: 253 AN: 5172

South Asian (SAS) AF: 0.0964 AC: 466 AN: 4834

European-Finnish (FIN) AF: 0.0812 AC: 860 AN: 10586

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8405 AN: 68020

Other (OTH) AF: 0.0935 AC: 197 AN: 2108

Alfa AF: 0.112 Hom.: 3285

Bravo AF: 0.0877

Asia WGS AF: 0.105 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.67
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7759295; hg19: chr6-41135850;