6-149152963-C-T

Variant names:

• chr6-149152963-C-T
• rs4073251
• ENST00000687816.2:n.182-8141C>T

Variant summary

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

The ENST00000687816.2(ENSG00000289359):​n.182-8141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,138 control chromosomes in the GnomAD database, including 2,430 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 0.17 (2430 hom., cov: 32)
• Consequence: ENSG00000289359 ENST00000687816.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 1 publications found

Genes affected

ENSG00000289359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901426	XR_007059807.1	n.152-3323C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289359	ENST00000687816.2	n.182-8141C>T		intron_variant	Intron 1 of 1
ENSG00000308521	ENST00000834740.1	n.228+15962G>A		intron_variant	Intron 2 of 3
ENSG00000289359	ENST00000834836.1	n.105-3323C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26294 AN: 152020 Hom.: 2434 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.173 AC: 26311 AN: 152138 Hom.: 2430 Cov.: 32 AF XY: 0.175 AC XY: 13032 AN XY: 74364

African (AFR) AF: 0.171 AC: 7111 AN: 41498

American (AMR) AF: 0.115 AC: 1751 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5178

South Asian (SAS) AF: 0.189 AC: 912 AN: 4820

European-Finnish (FIN) AF: 0.262 AC: 2778 AN: 10590

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12479 AN: 67986

Other (OTH) AF: 0.169 AC: 357 AN: 2110

Alfa AF: 0.164 Hom.: 355

Bravo AF: 0.158

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs4073251; hg19: chr6-149474099;