rs6845999

Variant names:

• chr4-144644674-C-T
• rs6845999
• ENST00000508269.3:n.282-940G>A

Variant summary

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

The ENST00000508269.3(HHIP-AS1):​n.282-940G>A 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 152,102 control chromosomes in the GnomAD database, including 10,804 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 (10804 hom., cov: 33)
• Consequence: HHIP-AS1 ENST00000508269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 26 publications found

Genes affected

HHIP-AS1 (HGNC:44182): (HHIP antisense RNA 1)

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HHIP-AS1	NR_037595.1	n.314-940G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-228696G>A		intron_variant	Intron 4 of 8			ENSP00000497507.1

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52973 AN: 151984 Hom.: 10806 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.348 AC: 52989 AN: 152102 Hom.: 10804 Cov.: 33 AF XY: 0.354 AC XY: 26296 AN XY: 74342

African (AFR) AF: 0.125 AC: 5168 AN: 41508

American (AMR) AF: 0.403 AC: 6164 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1476 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1100 AN: 5172

South Asian (SAS) AF: 0.519 AC: 2496 AN: 4810

European-Finnish (FIN) AF: 0.467 AC: 4943 AN: 10576

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30331 AN: 67968

Other (OTH) AF: 0.358 AC: 754 AN: 2104

Alfa AF: 0.421 Hom.: 41157

Bravo AF: 0.332

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.68
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs6845999; hg19: chr4-145565826;