rs4710758

chr6-170139836-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671798.1(ENSG00000288162):n.99-688C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,162 control chromosomes in the GnomAD database, including 5,466 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 0.25 (5466 hom., cov: 34)
• Consequence: ENST00000671798.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671798.1	n.99-688C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38103 AN: 152046 Hom.: 5451 Cov.: 34

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.251 AC: 38153 AN: 152162 Hom.: 5466 Cov.: 34 AF XY: 0.253 AC XY: 18786 AN XY: 74378

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.249

Alfa AF: 0.284 Hom.: 9975

Bravo AF: 0.242

Asia WGS AF: 0.283 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.52
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4710758; hg19: chr6-170455060;