rs705471

Variant names:

• chr10-3625534-A-G
• rs705471
• ENST00000737075.1:n.205+430T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000737075.1(ENSG00000296170):​n.205+430T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,004 control chromosomes in the GnomAD database, including 9,298 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 0.35 (9298 hom., cov: 32)
• Consequence: ENSG00000296170 ENST00000737075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 6 publications found

Genes affected

ENSG00000296170 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.163-123154A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296170	ENST00000737075.1	n.205+430T>C		intron_variant	Intron 1 of 3
ENSG00000296170	ENST00000737076.1	n.176+430T>C		intron_variant	Intron 1 of 3
ENSG00000296170	ENST00000737077.1	n.180+430T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52934 AN: 151888 Hom.: 9298 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.348 AC: 52944 AN: 152004 Hom.: 9298 Cov.: 32 AF XY: 0.342 AC XY: 25439 AN XY: 74294

African (AFR) AF: 0.308 AC: 12749 AN: 41454

American (AMR) AF: 0.383 AC: 5849 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1552 AN: 5180

South Asian (SAS) AF: 0.202 AC: 971 AN: 4804

European-Finnish (FIN) AF: 0.309 AC: 3259 AN: 10550

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25873 AN: 67970

Other (OTH) AF: 0.358 AC: 753 AN: 2106

Alfa AF: 0.372 Hom.: 47102

Bravo AF: 0.355

Asia WGS AF: 0.261 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	6.5
DANN	Benign	0.85
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs705471; hg19: chr10-3667726;