rs17064578

chr4-177300044-T-C

Variant summary

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

The ENST00000656694.1(ENSG00000287544):n.112+1003A>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 0.174 in 152,152 control chromosomes in the GnomAD database, including 2,905 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 (2905 hom., cov: 32)
• Consequence: ENST00000656694.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377557	XR_001741925.2	n.234+1003A>G		intron_variant, non_coding_transcript_variant
LOC105377557	XR_007058380.1	n.234+1003A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656694.1	n.112+1003A>G		intron_variant, non_coding_transcript_variant
	ENST00000662794.1	n.61+1003A>G		intron_variant, non_coding_transcript_variant
	ENST00000667713.1	n.207+1003A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26445 AN: 152034 Hom.: 2890 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.174 AC: 26494 AN: 152152 Hom.: 2905 Cov.: 32 AF XY: 0.175 AC XY: 13029 AN XY: 74392

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.144

Alfa AF: 0.119 Hom.: 1282

Bravo AF: 0.188

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17064578; hg19: chr4-178221198;