rs35205176

Variant names:

• chr7-51547455-T-A
• rs35205176
• ENST00000648455.1:n.194-22886T>A

Your query was ambiguous. Multiple possible variants found:

• chr7-51547455-T-A
• chr7-51547455-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648455.1(ENSG00000285741):​n.194-22886T>A variant causes a intron 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: ENSG00000285741 ENST00000648455.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 1 publications found

Genes affected

ENSG00000285741 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375277	XR_927260.4	n.355+2996T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285741	ENST00000648455.1	n.194-22886T>A		intron_variant	Intron 1 of 6
ENSG00000285741	ENST00000769890.1	n.204-22886T>A		intron_variant	Intron 2 of 8
ENSG00000285741	ENST00000769891.1	n.193-22886T>A		intron_variant	Intron 2 of 6
ENSG00000285741	ENST00000769892.1	n.200-22886T>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.211 AC: 8757 AN: 41474

American (AMR) AF: 0.254 AC: 3875 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3468

East Asian (EAS) AF: 0.178 AC: 919 AN: 5162

South Asian (SAS) AF: 0.297 AC: 1427 AN: 4812

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19371 AN: 67970

Other (OTH) AF: 0.249 AC: 524 AN: 2106

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs35205176; hg19: chr7-51615152;