rs10520358

Variant names:

• chr4-176666743-C-T
• rs10520358
• ENST00000504017.6:n.104-2878C>T

Variant summary

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

The ENST00000504017.6(HAFML):​n.104-2878C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0926 in 152,102 control chromosomes in the GnomAD database, including 712 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 0.093 (712 hom., cov: 32)
• Consequence: HAFML ENST00000504017.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 3 publications found

Genes affected

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

ENSG00000309713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504017.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAFML	NR_183975.1		n.94-2878C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAFML	ENST00000504017.6	TSL:2	n.104-2878C>T		intron	N/A
	HAFML	ENST00000509194.2	TSL:3	n.67-2878C>T		intron	N/A
	HAFML	ENST00000843108.1		n.105-2878C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14073 AN: 151984 Hom.: 712 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0645

Gnomad ASJ AF: 0.0969

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0295

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0858

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

GnomAD4 genome AF: 0.0926 AC: 14088 AN: 152102 Hom.: 712 Cov.: 32 AF XY: 0.0887 AC XY: 6597 AN XY: 74360

African (AFR) AF: 0.105 AC: 4349 AN: 41490

American (AMR) AF: 0.0644 AC: 983 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 336 AN: 3468

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4814

European-Finnish (FIN) AF: 0.0796 AC: 841 AN: 10564

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7045 AN: 68016

Other (OTH) AF: 0.0849 AC: 179 AN: 2108

Alfa AF: 0.101 Hom.: 1437

Bravo AF: 0.0928

Asia WGS AF: 0.0210 AC: 74 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs10520358; hg19: chr4-177587894;