rs17578222

Positions:

• chr7-51611603-C-A

Variant summary

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

The ENST00000648455.1(ENSG00000285741):​n.352+41104C>A 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 0.154 in 152,118 control chromosomes in the GnomAD database, including 2,223 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 (2223 hom., cov: 32)
• Consequence: ENST00000648455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648455.1	n.352+41104C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23453 AN: 152000 Hom.: 2223 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.154 AC: 23463 AN: 152118 Hom.: 2223 Cov.: 32 AF XY: 0.163 AC XY: 12116 AN XY: 74338

Gnomad4 AFR AF: 0.0573

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.158

Alfa AF: 0.169 Hom.: 4820

Bravo AF: 0.137

Asia WGS AF: 0.178 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17578222; hg19: chr7-51679299;