rs10407714

Positions:

• chr19-9208547-G-A

Variant summary

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

The ENST00000641088.1(ENSG00000290821):​n.4417G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,078 control chromosomes in the GnomAD database, including 8,940 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 (8940 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENST00000641088.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR7E24	XM_047438594.1	c.32+1525G>A		intron_variant			XP_047294550.1
OR7E24	XM_047438597.1	c.-207+1525G>A		intron_variant			XP_047294553.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641088.1	n.4417G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39170 AN: 151956 Hom.: 8890 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.0881

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.226

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.258 AC: 39275 AN: 152074 Hom.: 8940 Cov.: 32 AF XY: 0.258 AC XY: 19164 AN XY: 74352

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.0881

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.227

Alfa AF: 0.138 Hom.: 3319

Bravo AF: 0.279

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	-1.0
CADD	Benign	0.48
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10407714; hg19: chr19-9319223;