rs2046463

Variant names:

• chr4-176681548-G-A
• rs2046463
• ENST00000504017.6:n.243+1798G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-176681548-G-A
• chr4-176681548-G-C

Variant summary

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

The ENST00000504017.6(HAFML):​n.243+1798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,988 control chromosomes in the GnomAD database, including 28,203 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 0.58 (28203 hom., cov: 33)
• Consequence: HAFML ENST00000504017.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452
• Publications: 5 publications found

Genes affected

HAFML (HGNC:56694): (HuR (ELAVL1) associated fibroblast migratory lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAFML	NR_183975.1	n.182+11839G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAFML	ENST00000504017.6	n.243+1798G>A		intron_variant	Intron 3 of 3	2
HAFML	ENST00000509194.2	n.155+11839G>A		intron_variant	Intron 2 of 2	3
HAFML	ENST00000843108.1	n.193+11839G>A		intron_variant	Intron 2 of 2
HAFML	ENST00000843109.1	n.240+1798G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88720 AN: 151870 Hom.: 28213 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.584 AC: 88733 AN: 151988 Hom.: 28203 Cov.: 33 AF XY: 0.593 AC XY: 44067 AN XY: 74306

African (AFR) AF: 0.316 AC: 13083 AN: 41438

American (AMR) AF: 0.581 AC: 8867 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2341 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3624 AN: 5166

South Asian (SAS) AF: 0.736 AC: 3556 AN: 4830

European-Finnish (FIN) AF: 0.753 AC: 7942 AN: 10554

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47232 AN: 67942

Other (OTH) AF: 0.595 AC: 1259 AN: 2116

Alfa AF: 0.656 Hom.: 17645

Bravo AF: 0.557

Asia WGS AF: 0.698 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2046463; hg19: chr4-177602699;