rs17157642

chr7-110383304-A-G

Variant summary

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

The ENST00000667232.1(ENSG00000226965):n.412-18014T>C 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 0.146 in 152,212 control chromosomes in the GnomAD database, including 1,772 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 0.15 (1772 hom., cov: 32)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375451	XR_927863.3	n.387-18014T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667232.1	n.412-18014T>C		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.331-18014T>C		intron_variant, non_coding_transcript_variant
	ENST00000666128.1	n.98-18014T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22159 AN: 152094 Hom.: 1770 Cov.: 32

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.146 AC: 22170 AN: 152212 Hom.: 1772 Cov.: 32 AF XY: 0.149 AC XY: 11087 AN XY: 74414

Gnomad4 AFR AF: 0.0920

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.170

Alfa AF: 0.153 Hom.: 292

Bravo AF: 0.135

Asia WGS AF: 0.228 AC: 791 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	1.5
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17157642; hg19: chr7-110023361;