rs9904761

Variant names:

• chr17-48879468-C-G
• rs9904761
• ENST00000508743.2:n.477-123G>C

Variant summary

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

The ENST00000508743.2(ENSG00000293025):​n.477-123G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,046 control chromosomes in the GnomAD database, including 8,506 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 0.33 (8496 hom., cov: 31)
  • Exomes 𝑓: 0.29 (10 hom.)
• Consequence: ENSG00000293025 ENST00000508743.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.441
• Publications: 10 publications found

Genes affected

ENSG00000293025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371814	NR_135674.1	n.477-123G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293025	ENST00000508743.2	n.477-123G>C		intron_variant	Intron 2 of 3	3
ENSG00000293025	ENST00000817118.1	n.145-123G>C		intron_variant	Intron 1 of 2
ENSG00000293025	ENST00000817119.1	n.133-123G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49895 AN: 151678 Hom.: 8479 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.288 AC: 72 AN: 250 Hom.: 10 AF XY: 0.261 AC XY: 47 AN XY: 180

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 2 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.389 AC: 7 AN: 18

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.306 AC: 57 AN: 186

Other (OTH) AF: 0.125 AC: 3 AN: 24

GnomAD4 genome AF: 0.329 AC: 49960 AN: 151796 Hom.: 8496 Cov.: 31 AF XY: 0.330 AC XY: 24446 AN XY: 74188

African (AFR) AF: 0.363 AC: 14987 AN: 41342

American (AMR) AF: 0.445 AC: 6778 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.166 AC: 860 AN: 5168

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4816

European-Finnish (FIN) AF: 0.270 AC: 2849 AN: 10558

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 20971 AN: 67908

Other (OTH) AF: 0.332 AC: 697 AN: 2102

Alfa AF: 0.325 Hom.: 1026

Bravo AF: 0.344

Asia WGS AF: 0.213 AC: 743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.1
DANN	Benign	0.68
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs9904761; hg19: chr17-46956830;