rs10520358

Positions:

• chr4-176666743-C-T

Variant summary

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

The NR_183975.1(HAFML):​n.94-2878C>T 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 0.0926 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 NR_183975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585

Genes affected

HAFML (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 (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAFML	NR_183975.1	n.94-2878C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0644

Gnomad4 ASJ AF: 0.0969

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.102 Hom.: 1058

Bravo AF: 0.0928

Asia WGS AF: 0.0210 AC: 74 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520358; hg19: chr4-177587894;