rs35205176

Positions:

• chr7-51547455-T-A

Variant summary

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

The ENST00000648455.1(ENSG00000285741):​n.194-22886T>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 0.257 in 152,056 control chromosomes in the GnomAD database, including 5,119 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 0.26 (5119 hom., cov: 32)
• Consequence: ENST00000648455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375277	XR_927260.4	n.355+2996T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648455.1	n.194-22886T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39052 AN: 151938 Hom.: 5115 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.257 AC: 39080 AN: 152056 Hom.: 5119 Cov.: 32 AF XY: 0.257 AC XY: 19090 AN XY: 74336

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.249

Alfa AF: 0.259 Hom.: 643

Bravo AF: 0.255

Asia WGS AF: 0.225 AC: 784 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	0.53
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: rs35205176; hg19: chr7-51615152;