rs708384

Positions:

• chr17-44360314-C-A
• chr17-44360314-C-T

Variant summary

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

The NM_198475.3(FAM171A2):​c.119-182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,142 control chromosomes in the GnomAD database, including 18,232 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 0.46 (18232 hom., cov: 33)
• Consequence: FAM171A2 NM_198475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

FAM171A2 (HGNC:30480): (family with sequence similarity 171 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM171A2	NM_198475.3	c.119-182G>T		intron_variant		ENST00000293443.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM171A2	ENST00000293443.12	c.119-182G>T		intron_variant		1	NM_198475.3	P1
FAM171A2	ENST00000588067.1	c.119-182G>T		intron_variant, NMD_transcript_variant		5
FAM171A2	ENST00000589407.5	c.119-182G>T		intron_variant, NMD_transcript_variant		3
FAM171A2	ENST00000592560.1	n.205-182G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70182 AN: 152024 Hom.: 18209 Cov.: 33

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.462 AC: 70245 AN: 152142 Hom.: 18232 Cov.: 33 AF XY: 0.456 AC XY: 33921 AN XY: 74370

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.402

Alfa AF: 0.359 Hom.: 14237

Bravo AF: 0.463

Asia WGS AF: 0.382 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs708384; hg19: chr17-42437682;