chr6-3467990-T-C

Variant names:

• chr6-3467990-T-C
• rs7775474
• ENST00000754968.1:n.582-896T>C

Variant summary

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

The ENST00000754968.1(ENSG00000298336):​n.582-896T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,058 control chromosomes in the GnomAD database, including 25,656 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 0.57 (25656 hom., cov: 32)
• Consequence: ENSG00000298336 ENST00000754968.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 5 publications found

Genes affected

ENSG00000298336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC643327	NR_147844.1	n.550-896T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298336	ENST00000754968.1	n.582-896T>C		intron_variant	Intron 1 of 1
ENSG00000298336	ENST00000754969.1	n.496-896T>C		intron_variant	Intron 2 of 2
ENSG00000298336	ENST00000754970.1	n.688-896T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86419 AN: 151940 Hom.: 25619 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.569 AC: 86506 AN: 152058 Hom.: 25656 Cov.: 32 AF XY: 0.565 AC XY: 41990 AN XY: 74332

African (AFR) AF: 0.729 AC: 30234 AN: 41480

American (AMR) AF: 0.471 AC: 7205 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3468

East Asian (EAS) AF: 0.509 AC: 2636 AN: 5180

South Asian (SAS) AF: 0.723 AC: 3490 AN: 4830

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10558

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34735 AN: 67946

Other (OTH) AF: 0.560 AC: 1179 AN: 2104

Alfa AF: 0.531 Hom.: 86723

Bravo AF: 0.573

Asia WGS AF: 0.593 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.39
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs7775474; hg19: chr6-3468224;