rs1046332

chr1-149845941-T-C

Variant summary

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

The ENST00000564237.2(ENSG00000290792):n.4997A>G 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 0.0499 in 152,260 control chromosomes in the GnomAD database, including 252 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 0.050 (252 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000564237.2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
H4C15	XM_024451708.2	c.*9145A>G		3_prime_UTR_variant	2/2
H4C15	XM_047424434.1	c.*9715A>G		3_prime_UTR_variant	3/3
H4C15	XM_047424439.1	c.*9359A>G		3_prime_UTR_variant	3/3
H4C15	XM_047424442.1	c.*8965A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000564237.2	n.4997A>G		non_coding_transcript_exon_variant	1/1
	ENST00000608318.2	n.3067T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7595 AN: 152140 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.0499 AC: 7595 AN: 152258 Hom.: 252 Cov.: 32 AF XY: 0.0479 AC XY: 3566 AN XY: 74436

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0723

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00974

Gnomad4 FIN AF: 0.0671

Gnomad4 NFE AF: 0.0786

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0680 Hom.: 125

Bravo AF: 0.0465

Asia WGS AF: 0.00635 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.4
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1046332; hg19: chr1-149817508;