rs12510099

Positions:

• chr4-176681802-G-A

Variant summary

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

The NR_183975.1(HAFML):​n.182+12093G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0837 in 152,146 control chromosomes in the GnomAD database, including 592 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 0.084 (592 hom., cov: 32)
• Consequence: HAFML NR_183975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HAFML	NR_183975.1	n.182+12093G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAFML	ENST00000509194.1	n.89+12093G>A		intron_variant, non_coding_transcript_variant		3
HAFML	ENST00000504017.5	n.140+2052G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0838 AC: 12733 AN: 152030 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0967

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0837 AC: 12742 AN: 152146 Hom.: 592 Cov.: 32 AF XY: 0.0802 AC XY: 5967 AN XY: 74376

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0967

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0806

Alfa AF: 0.100 Hom.: 96

Bravo AF: 0.0829

Asia WGS AF: 0.0200 AC: 71 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12510099; hg19: chr4-177602953;