rs17563605

chr6-126843427-T-C

Variant summary

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

The ENST00000651326.1(ENSG00000293110):n.693+160758A>G 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 0.18 in 152,058 control chromosomes in the GnomAD database, including 3,072 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 0.18 (3072 hom., cov: 32)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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
	ENST00000651326.1	n.693+160758A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27367 AN: 151940 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.0712

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.180 AC: 27389 AN: 152058 Hom.: 3072 Cov.: 32 AF XY: 0.175 AC XY: 12978 AN XY: 74344

Gnomad4 AFR AF: 0.0711

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0215

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.185

Alfa AF: 0.238 Hom.: 4281

Bravo AF: 0.173

Asia WGS AF: 0.156 AC: 543 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17563605; hg19: chr6-127164572;